SRX5496699 GSM3664143 SRP187977 SRS4466301 GSM3664143 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664143 GSM3664143 GEO Accession GSM3664143 SRX5496700 GSM3664144 SRP187977 SRS4466302 GSM3664144 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664144 GSM3664144 GEO Accession GSM3664144 SRX5496701 GSM3664145 SRP187977 SRS4466303 GSM3664145 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664145 GSM3664145 GEO Accession GSM3664145 SRX5496702 GSM3664146 SRP187977 SRS4466304 GSM3664146 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664146 GSM3664146 GEO Accession GSM3664146 SRX5496703 GSM3664147 SRP187977 SRS4466305 GSM3664147 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664147 GSM3664147 GEO Accession GSM3664147 SRX5496704 GSM3664148 SRP187977 SRS4466306 GSM3664148 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664148 GSM3664148 GEO Accession GSM3664148 SRX5496705 GSM3664149 SRP187977 SRS4466307 GSM3664149 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664149 GSM3664149 GEO Accession GSM3664149 SRX5496706 GSM3664150 SRP187977 SRS4466308 GSM3664150 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664150 GSM3664150 GEO Accession GSM3664150 SRX5496707 GSM3664159 SRP187977 SRS4466309 GSM3664159 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664159 GSM3664159 GEO Accession GSM3664159 SRX5496708 GSM3664160 SRP187977 SRS4466310 GSM3664160 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664160 GSM3664160 GEO Accession GSM3664160 SRX5496709 GSM3664161 SRP187977 SRS4466311 GSM3664161 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664161 GSM3664161 GEO Accession GSM3664161 SRX5496710 GSM3664162 SRP187977 SRS4466312 GSM3664162 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664162 GSM3664162 GEO Accession GSM3664162 SRX5496711 GSM3664163 SRP187977 SRS4466313 GSM3664163 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664163 GSM3664163 GEO Accession GSM3664163 SRX5496712 GSM3664164 SRP187977 SRS4466314 GSM3664164 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664164 GSM3664164 GEO Accession GSM3664164 SRX5496713 GSM3664165 SRP187977 SRS4466315 GSM3664165 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664165 GSM3664165 GEO Accession GSM3664165 SRX5496714 GSM3664166 SRP187977 SRS4466316 GSM3664166 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664166 GSM3664166 GEO Accession GSM3664166 SRX5496715 GSM3664167 SRP187977 SRS4466317 GSM3664167 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664167 GSM3664167 GEO Accession GSM3664167 SRX5496716 GSM3664168 SRP187977 SRS4466318 GSM3664168 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664168 GSM3664168 GEO Accession GSM3664168 SRX5496717 GSM3664169 SRP187977 SRS4466319 GSM3664169 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664169 GSM3664169 GEO Accession GSM3664169 SRX5496718 GSM3664170 SRP187977 SRS4466320 GSM3664170 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664170 GSM3664170 GEO Accession GSM3664170 SRX5496719 GSM3664171 SRP187977 SRS4466321 GSM3664171 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664171 GSM3664171 GEO Accession GSM3664171 SRX5496720 GSM3664172 SRP187977 SRS4466322 GSM3664172 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664172 GSM3664172 GEO Accession GSM3664172 SRX5496721 GSM3664173 SRP187977 SRS4466323 GSM3664173 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664173 GSM3664173 GEO Accession GSM3664173 SRX5496722 GSM3664174 SRP187977 SRS4466324 GSM3664174 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664174 GSM3664174 GEO Accession GSM3664174 SRX5496723 GSM3664175 SRP187977 SRS4466325 GSM3664175 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664175 GSM3664175 GEO Accession GSM3664175 SRX5496724 GSM3664176 SRP187977 SRS4466326 GSM3664176 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664176 GSM3664176 GEO Accession GSM3664176 SRX5496725 GSM3664177 SRP187977 SRS4466327 GSM3664177 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664177 GSM3664177 GEO Accession GSM3664177 SRX5496726 GSM3664178 SRP187977 SRS4466328 GSM3664178 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664178 GSM3664178 GEO Accession GSM3664178 SRX5496727 GSM3664179 SRP187977 SRS4466329 GSM3664179 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664179 GSM3664179 GEO Accession GSM3664179 SRX5496728 GSM3664180 SRP187977 SRS4466330 GSM3664180 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664180 GSM3664180 GEO Accession GSM3664180 SRX5496729 GSM3664181 SRP187977 SRS4466331 GSM3664181 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664181 GSM3664181 GEO Accession GSM3664181 SRX5496730 GSM3664182 SRP187977 SRS4466332 GSM3664182 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664182 GSM3664182 GEO Accession GSM3664182 SRX5496731 GSM3664183 SRP187977 SRS4466333 GSM3664183 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664183 GSM3664183 GEO Accession GSM3664183 SRX5496732 GSM3664184 SRP187977 SRS4466334 GSM3664184 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664184 GSM3664184 GEO Accession GSM3664184 SRX5496733 GSM3664185 SRP187977 SRS4466335 GSM3664185 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664185 GSM3664185 GEO Accession GSM3664185 SRX5496734 GSM3664186 SRP187977 SRS4466336 GSM3664186 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664186 GSM3664186 GEO Accession GSM3664186 SRX5496735 GSM3664187 SRP187977 SRS4466337 GSM3664187 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664187 GSM3664187 GEO Accession GSM3664187 SRX5496736 GSM3664188 SRP187977 SRS4466338 GSM3664188 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664188 GSM3664188 GEO Accession GSM3664188 SRX5496737 GSM3664189 SRP187977 SRS4466339 GSM3664189 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664189 GSM3664189 GEO Accession GSM3664189 SRX5496738 GSM3664190 SRP187977 SRS4466340 GSM3664190 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664190 GSM3664190 GEO Accession GSM3664190 SRX5496739 GSM3664191 SRP187977 SRS4466341 GSM3664191 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664191 GSM3664191 GEO Accession GSM3664191 SRX5496740 GSM3664192 SRP187977 SRS4466342 GSM3664192 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664192 GSM3664192 GEO Accession GSM3664192 SRX5496741 GSM3664193 SRP187977 SRS4466343 GSM3664193 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664193 GSM3664193 GEO Accession GSM3664193 SRX5496742 GSM3664194 SRP187977 SRS4466344 GSM3664194 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664194 GSM3664194 GEO Accession GSM3664194 SRX5496743 GSM3664195 SRP187977 SRS4466345 GSM3664195 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664195 GSM3664195 GEO Accession GSM3664195 SRX5496744 GSM3664196 SRP187977 SRS4466346 GSM3664196 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664196 GSM3664196 GEO Accession GSM3664196 SRX5496745 GSM3664197 SRP187977 SRS4466347 GSM3664197 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664197 GSM3664197 GEO Accession GSM3664197 SRX5496746 GSM3664198 SRP187977 SRS4466348 GSM3664198 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664198 GSM3664198 GEO Accession GSM3664198 SRX5496747 GSM3664199 SRP187977 SRS4466349 GSM3664199 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664199 GSM3664199 GEO Accession GSM3664199 SRX5496748 GSM3664200 SRP187977 SRS4466350 GSM3664200 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664200 GSM3664200 GEO Accession GSM3664200 SRX5496749 GSM3664201 SRP187977 SRS4466351 GSM3664201 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664201 GSM3664201 GEO Accession GSM3664201 SRX5496750 GSM3664202 SRP187977 SRS4466352 GSM3664202 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664202 GSM3664202 GEO Accession GSM3664202 SRX5496751 GSM3664203 SRP187977 SRS4466353 GSM3664203 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664203 GSM3664203 GEO Accession GSM3664203 SRX5496752 GSM3664204 SRP187977 SRS4466354 GSM3664204 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664204 GSM3664204 GEO Accession GSM3664204 SRX5496753 GSM3664205 SRP187977 SRS4466355 GSM3664205 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664205 GSM3664205 GEO Accession GSM3664205 SRX5496754 GSM3664206 SRP187977 SRS4466356 GSM3664206 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664206 GSM3664206 GEO Accession GSM3664206 SRX5496755 GSM3664207 SRP187977 SRS4466357 GSM3664207 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664207 GSM3664207 GEO Accession GSM3664207 SRX5496756 GSM3664208 SRP187977 SRS4466358 GSM3664208 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664208 GSM3664208 GEO Accession GSM3664208 SRX5496757 GSM3664209 SRP187977 SRS4466359 GSM3664209 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664209 GSM3664209 GEO Accession GSM3664209 SRX5496758 GSM3664210 SRP187977 SRS4466360 GSM3664210 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664210 GSM3664210 GEO Accession GSM3664210 SRX5496759 GSM3664211 SRP187977 SRS4466361 GSM3664211 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664211 GSM3664211 GEO Accession GSM3664211 SRX5496760 GSM3664212 SRP187977 SRS4466362 GSM3664212 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664212 GSM3664212 GEO Accession GSM3664212 SRX5496761 GSM3664213 SRP187977 SRS4466363 GSM3664213 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664213 GSM3664213 GEO Accession GSM3664213 SRX5496762 GSM3664214 SRP187977 SRS4466364 GSM3664214 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664214 GSM3664214 GEO Accession GSM3664214 SRX5496763 GSM3664215 SRP187977 SRS4466365 GSM3664215 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664215 GSM3664215 GEO Accession GSM3664215 SRX5496764 GSM3664216 SRP187977 SRS4466366 GSM3664216 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664216 GSM3664216 GEO Accession GSM3664216 SRX5496765 GSM3664217 SRP187977 SRS4466367 GSM3664217 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664217 GSM3664217 GEO Accession GSM3664217 SRX5496766 GSM3664218 SRP187977 SRS4466368 GSM3664218 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664218 GSM3664218 GEO Accession GSM3664218 SRX5496767 GSM3664219 SRP187977 SRS4466369 GSM3664219 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664219 GSM3664219 GEO Accession GSM3664219 SRX5496768 GSM3664220 SRP187977 SRS4466370 GSM3664220 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664220 GSM3664220 GEO Accession GSM3664220 SRX5496769 GSM3664221 SRP187977 SRS4466371 GSM3664221 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664221 GSM3664221 GEO Accession GSM3664221 SRX5496770 GSM3664222 SRP187977 SRS4466372 GSM3664222 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664222 GSM3664222 GEO Accession GSM3664222 SRX5496771 GSM3664223 SRP187977 SRS4466373 GSM3664223 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664223 GSM3664223 GEO Accession GSM3664223 SRX5496772 GSM3664224 SRP187977 SRS4466374 GSM3664224 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664224 GSM3664224 GEO Accession GSM3664224 SRX5496773 GSM3664225 SRP187977 SRS4466375 GSM3664225 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664225 GSM3664225 GEO Accession GSM3664225 SRX5496774 GSM3664226 SRP187977 SRS4466376 GSM3664226 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664226 GSM3664226 GEO Accession GSM3664226 SRX5496775 GSM3664227 SRP187977 SRS4466377 GSM3664227 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664227 GSM3664227 GEO Accession GSM3664227 SRX5496776 GSM3664228 SRP187977 SRS4466378 GSM3664228 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664228 GSM3664228 GEO Accession GSM3664228 SRX5496777 GSM3664229 SRP187977 SRS4466379 GSM3664229 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664229 GSM3664229 GEO Accession GSM3664229 SRX5496778 GSM3664230 SRP187977 SRS4466380 GSM3664230 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664230 GSM3664230 GEO Accession GSM3664230 SRX5496779 GSM3664231 SRP187977 SRS4466381 GSM3664231 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664231 GSM3664231 GEO Accession GSM3664231 SRX5496780 GSM3664232 SRP187977 SRS4466382 GSM3664232 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664232 GSM3664232 GEO Accession GSM3664232 SRX5496781 GSM3664233 SRP187977 SRS4466383 GSM3664233 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664233 GSM3664233 GEO Accession GSM3664233 SRX5496782 GSM3664234 SRP187977 SRS4466384 GSM3664234 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664234 GSM3664234 GEO Accession GSM3664234 SRX5496783 GSM3664235 SRP187977 SRS4466385 GSM3664235 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664235 GSM3664235 GEO Accession GSM3664235 SRX5496784 GSM3664236 SRP187977 SRS4466386 GSM3664236 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664236 GSM3664236 GEO Accession GSM3664236 SRX5496785 GSM3664151 SRP187977 SRS4466387 GSM3664151 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664151 GSM3664151 GEO Accession GSM3664151 SRX5496786 GSM3664152 SRP187977 SRS4466388 GSM3664152 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664152 GSM3664152 GEO Accession GSM3664152 SRX5496787 GSM3664153 SRP187977 SRS4466389 GSM3664153 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664153 GSM3664153 GEO Accession GSM3664153 SRX5496788 GSM3664154 SRP187977 SRS4466390 GSM3664154 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664154 GSM3664154 GEO Accession GSM3664154 SRX5496789 GSM3664155 SRP187977 SRS4466391 GSM3664155 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664155 GSM3664155 GEO Accession GSM3664155 SRX5496790 GSM3664156 SRP187977 SRS4466392 GSM3664156 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664156 GSM3664156 GEO Accession GSM3664156 SRX5496791 GSM3664157 SRP187977 SRS4466393 GSM3664157 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664157 GSM3664157 GEO Accession GSM3664157 SRX5496792 GSM3664158 SRP187977 SRS4466394 GSM3664158 RNA-Seq TRANSCRIPTOMIC cDNA 94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover. Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer's protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads). Illumina HiSeq 4000 gds 303664158 GSM3664158 GEO Accession GSM3664158