SRX23577427 GSM8069905_r1 SRP488960 PRJNA1074709 SRS20422635 GSM8069905 GSM8069905 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA 16 (day7) to 32 (day3) notoroids were dissociated by first washing with PBS-/- and then incubating with accutase for 10min at 37°C following mechanical dissociation and another incubation at 37°C. Accutase suspension was then diluted in 4x volume with resuspension buffer (DMEM/F12 with 1% BSA). The cell suspension was then spined for 4min at 0.6xg, resuspended in 250µL of resuspension buffer and filtered through a 40µm Flowmi cell strainer (cat. no. 136800040) and twice through a pre-wet 20µm pluriSelect strainer (43-10020-60). The single-cell suspension was diluted to 1300 cells/uL and had a viability >95%. The samples were separately loaded for capture with the Chromium System using the Single Cell 3′ v3.1 reagents (10X Genomics). cDNA amplification involved 12 PCR cycles. Libraries for the samples were multiplexed so that the number of reads matched one lane per sample and sequenced on an Illumina HiSeq4000 using 100 bp paired-end runs. Illumina HiSeq 4000 SRX23577428 GSM8069906_r1 SRP488960 PRJNA1074709 SRS20422638 GSM8069906 GSM8069906 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA 16 (day7) to 32 (day3) notoroids were dissociated by first washing with PBS-/- and then incubating with accutase for 10min at 37°C following mechanical dissociation and another incubation at 37°C. Accutase suspension was then diluted in 4x volume with resuspension buffer (DMEM/F12 with 1% BSA). The cell suspension was then spined for 4min at 0.6xg, resuspended in 250µL of resuspension buffer and filtered through a 40µm Flowmi cell strainer (cat. no. 136800040) and twice through a pre-wet 20µm pluriSelect strainer (43-10020-60). The single-cell suspension was diluted to 1300 cells/uL and had a viability >95%. The samples were separately loaded for capture with the Chromium System using the Single Cell 3′ v3.1 reagents (10X Genomics). cDNA amplification involved 12 PCR cycles. Libraries for the samples were multiplexed so that the number of reads matched one lane per sample and sequenced on an Illumina HiSeq4000 using 100 bp paired-end runs. Illumina HiSeq 4000 SRX23577429 GSM8069908_r1 SRP488960 PRJNA1074709 SRS20422636 GSM8069908 GSM8069908 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA 16 (day7) to 32 (day3) notoroids were dissociated by first washing with PBS-/- and then incubating with accutase for 10min at 37°C following mechanical dissociation and another incubation at 37°C. Accutase suspension was then diluted in 4x volume with resuspension buffer (DMEM/F12 with 1% BSA). The cell suspension was then spined for 4min at 0.6xg, resuspended in 250µL of resuspension buffer and filtered through a 40µm Flowmi cell strainer (cat. no. 136800040) and twice through a pre-wet 20µm pluriSelect strainer (43-10020-60). The single-cell suspension was diluted to 1300 cells/uL and had a viability >95%. The samples were separately loaded for capture with the Chromium System using the Single Cell 3′ v3.1 reagents (10X Genomics). cDNA amplification involved 12 PCR cycles. Libraries for the samples were multiplexed so that the number of reads matched one lane per sample and sequenced on an Illumina HiSeq4000 using 100 bp paired-end runs. Illumina HiSeq 4000 SRX23577430 GSM8069909_r1 SRP488960 PRJNA1074709 SRS20422639 GSM8069909 GSM8069909 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA 16 (day7) to 32 (day3) notoroids were dissociated by first washing with PBS-/- and then incubating with accutase for 10min at 37°C following mechanical dissociation and another incubation at 37°C. Accutase suspension was then diluted in 4x volume with resuspension buffer (DMEM/F12 with 1% BSA). The cell suspension was then spined for 4min at 0.6xg, resuspended in 250µL of resuspension buffer and filtered through a 40µm Flowmi cell strainer (cat. no. 136800040) and twice through a pre-wet 20µm pluriSelect strainer (43-10020-60). The single-cell suspension was diluted to 1300 cells/uL and had a viability >95%. The samples were separately loaded for capture with the Chromium System using the Single Cell 3′ v3.1 reagents (10X Genomics). cDNA amplification involved 12 PCR cycles. Libraries for the samples were multiplexed so that the number of reads matched one lane per sample and sequenced on an Illumina HiSeq4000 using 100 bp paired-end runs. Illumina HiSeq 4000 SRX23577431 GSM8069910_r1 SRP488960 PRJNA1074709 SRS20422640 GSM8069910 GSM8069910 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA 16 (day7) to 32 (day3) notoroids were dissociated by first washing with PBS-/- and then incubating with accutase for 10min at 37°C following mechanical dissociation and another incubation at 37°C. Accutase suspension was then diluted in 4x volume with resuspension buffer (DMEM/F12 with 1% BSA). The cell suspension was then spined for 4min at 0.6xg, resuspended in 250µL of resuspension buffer and filtered through a 40µm Flowmi cell strainer (cat. no. 136800040) and twice through a pre-wet 20µm pluriSelect strainer (43-10020-60). The single-cell suspension was diluted to 1300 cells/uL and had a viability >95%. The samples were separately loaded for capture with the Chromium System using the Single Cell 3′ v3.1 reagents (10X Genomics). cDNA amplification involved 12 PCR cycles. Libraries for the samples were multiplexed so that the number of reads matched one lane per sample and sequenced on an Illumina HiSeq4000 using 100 bp paired-end runs. Illumina HiSeq 4000 SRX23577432 GSM8069912_r1 SRP488960 PRJNA1074709 SRS20422637 GSM8069912 GSM8069912 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA 16 (day7) to 32 (day3) notoroids were dissociated by first washing with PBS-/- and then incubating with accutase for 10min at 37°C following mechanical dissociation and another incubation at 37°C. Accutase suspension was then diluted in 4x volume with resuspension buffer (DMEM/F12 with 1% BSA). The cell suspension was then spined for 4min at 0.6xg, resuspended in 250µL of resuspension buffer and filtered through a 40µm Flowmi cell strainer (cat. no. 136800040) and twice through a pre-wet 20µm pluriSelect strainer (43-10020-60). The single-cell suspension was diluted to 1300 cells/uL and had a viability >95%. The samples were separately loaded for capture with the Chromium System using the Single Cell 3′ v3.1 reagents (10X Genomics). cDNA amplification involved 12 PCR cycles. Libraries for the samples were multiplexed so that the number of reads matched one lane per sample and sequenced on an Illumina HiSeq4000 using 100 bp paired-end runs. Illumina HiSeq 4000 SRX23577433 GSM8069913_r1 SRP488960 PRJNA1074709 SRS20422641 GSM8069913 GSM8069913 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA 16 (day7) to 32 (day3) notoroids were dissociated by first washing with PBS-/- and then incubating with accutase for 10min at 37°C following mechanical dissociation and another incubation at 37°C. Accutase suspension was then diluted in 4x volume with resuspension buffer (DMEM/F12 with 1% BSA). The cell suspension was then spined for 4min at 0.6xg, resuspended in 250µL of resuspension buffer and filtered through a 40µm Flowmi cell strainer (cat. no. 136800040) and twice through a pre-wet 20µm pluriSelect strainer (43-10020-60). The single-cell suspension was diluted to 1300 cells/uL and had a viability >95%. The samples were separately loaded for capture with the Chromium System using the Single Cell 3′ v3.1 reagents (10X Genomics). cDNA amplification involved 12 PCR cycles. Libraries for the samples were multiplexed so that the number of reads matched one lane per sample and sequenced on an Illumina HiSeq4000 using 100 bp paired-end runs. Illumina HiSeq 4000