SRX647646 GSM1429227 SRP044135 SRS654930 GSM1429227 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429227 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429227 gds 301429227 GEO Accession GSM1429227 SRX647647 GSM1429228 SRP044135 SRS654931 GSM1429228 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429228 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429228 gds 301429228 GEO Accession GSM1429228 SRX647648 GSM1429229 SRP044135 SRS654932 GSM1429229 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429229 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429229 gds 301429229 GEO Accession GSM1429229 SRX647649 GSM1429230 SRP044135 SRS654934 GSM1429230 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429230 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429230 gds 301429230 GEO Accession GSM1429230 SRX647650 GSM1429231 SRP044135 SRS654933 GSM1429231 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429231 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429231 gds 301429231 GEO Accession GSM1429231 SRX647651 GSM1429232 SRP044135 SRS654935 GSM1429232 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429232 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429232 gds 301429232 GEO Accession GSM1429232 SRX647652 GSM1429233 SRP044135 SRS654936 GSM1429233 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429233 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429233 gds 301429233 GEO Accession GSM1429233 SRX647653 GSM1429234 SRP044135 SRS654939 GSM1429234 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429234 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429234 gds 301429234 GEO Accession GSM1429234 SRX647654 GSM1429235 SRP044135 SRS654938 GSM1429235 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429235 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429235 gds 301429235 GEO Accession GSM1429235 SRX647655 GSM1429236 SRP044135 SRS654937 GSM1429236 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429236 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429236 gds 301429236 GEO Accession GSM1429236 SRX647656 GSM1429237 SRP044135 SRS654940 GSM1429237 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429237 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429237 gds 301429237 GEO Accession GSM1429237 SRX647657 GSM1429238 SRP044135 SRS654942 GSM1429238 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429238 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429238 gds 301429238 GEO Accession GSM1429238 SRX647658 GSM1429239 SRP044135 SRS654941 GSM1429239 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429239 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429239 gds 301429239 GEO Accession GSM1429239 SRX647659 GSM1429240 SRP044135 SRS654944 GSM1429240 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429240 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429240 gds 301429240 GEO Accession GSM1429240 SRX647660 GSM1429241 SRP044135 SRS654943 GSM1429241 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429241 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429241 gds 301429241 GEO Accession GSM1429241 SRX647661 GSM1429242 SRP044135 SRS654945 GSM1429242 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429242 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429242 gds 301429242 GEO Accession GSM1429242 SRX647662 GSM1429243 SRP044135 SRS654946 GSM1429243 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429243 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429243 gds 301429243 GEO Accession GSM1429243 SRX647663 GSM1429244 SRP044135 SRS654947 GSM1429244 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429244 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429244 gds 301429244 GEO Accession GSM1429244 SRX647664 GSM1429245 SRP044135 SRS654948 GSM1429245 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429245 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429245 gds 301429245 GEO Accession GSM1429245 SRX647665 GSM1429246 SRP044135 SRS654949 GSM1429246 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429246 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429246 gds 301429246 GEO Accession GSM1429246 SRX647666 GSM1429247 SRP044135 SRS654950 GSM1429247 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429247 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429247 gds 301429247 GEO Accession GSM1429247 SRX647667 GSM1429248 SRP044135 SRS654951 GSM1429248 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429248 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429248 gds 301429248 GEO Accession GSM1429248 SRX647668 GSM1429249 SRP044135 SRS654952 GSM1429249 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429249 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429249 gds 301429249 GEO Accession GSM1429249 SRX647669 GSM1429250 SRP044135 SRS654953 GSM1429250 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429250 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429250 gds 301429250 GEO Accession GSM1429250 SRX647670 GSM1429251 SRP044135 SRS654954 GSM1429251 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429251 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429251 gds 301429251 GEO Accession GSM1429251 SRX647671 GSM1429252 SRP044135 SRS654955 GSM1429252 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429252 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429252 gds 301429252 GEO Accession GSM1429252 SRX647672 GSM1429253 SRP044135 SRS654956 GSM1429253 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429253 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429253 gds 301429253 GEO Accession GSM1429253 SRX647673 GSM1429254 SRP044135 SRS654957 GSM1429254 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429254 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429254 gds 301429254 GEO Accession GSM1429254 SRX647674 GSM1429255 SRP044135 SRS654958 GSM1429255 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429255 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429255 gds 301429255 GEO Accession GSM1429255 SRX647675 GSM1429256 SRP044135 SRS654959 GSM1429256 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429256 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429256 gds 301429256 GEO Accession GSM1429256 SRX647676 GSM1429257 SRP044135 SRS654960 GSM1429257 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429257 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429257 gds 301429257 GEO Accession GSM1429257 SRX647677 GSM1429258 SRP044135 SRS654961 GSM1429258 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429258 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429258 gds 301429258 GEO Accession GSM1429258 SRX647678 GSM1429259 SRP044135 SRS654962 GSM1429259 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429259 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429259 gds 301429259 GEO Accession GSM1429259 SRX647679 GSM1429260 SRP044135 SRS654963 GSM1429260 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429260 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429260 gds 301429260 GEO Accession GSM1429260 SRX647680 GSM1429261 SRP044135 SRS654964 GSM1429261 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429261 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429261 gds 301429261 GEO Accession GSM1429261 SRX647681 GSM1429262 SRP044135 SRS654966 GSM1429262 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429262 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429262 gds 301429262 GEO Accession GSM1429262 SRX647682 GSM1429263 SRP044135 SRS654965 GSM1429263 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429263 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429263 gds 301429263 GEO Accession GSM1429263 SRX647683 GSM1429264 SRP044135 SRS654967 GSM1429264 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429264 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429264 gds 301429264 GEO Accession GSM1429264 SRX647684 GSM1429265 SRP044135 SRS654968 GSM1429265 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429265 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429265 gds 301429265 GEO Accession GSM1429265 SRX647685 GSM1429266 SRP044135 SRS654969 GSM1429266 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429266 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429266 gds 301429266 GEO Accession GSM1429266 SRX647686 GSM1429267 SRP044135 SRS654970 GSM1429267 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429267 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429267 gds 301429267 GEO Accession GSM1429267 SRX647687 GSM1429268 SRP044135 SRS654971 GSM1429268 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429268 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429268 gds 301429268 GEO Accession GSM1429268 SRX647688 GSM1429269 SRP044135 SRS654972 GSM1429269 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429269 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429269 gds 301429269 GEO Accession GSM1429269 SRX647689 GSM1429270 SRP044135 SRS654973 GSM1429270 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429270 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429270 gds 301429270 GEO Accession GSM1429270 SRX647690 GSM1429271 SRP044135 SRS654975 GSM1429271 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429271 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429271 gds 301429271 GEO Accession GSM1429271 SRX647691 GSM1429272 SRP044135 SRS654974 GSM1429272 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429272 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429272 gds 301429272 GEO Accession GSM1429272 SRX647692 GSM1429273 SRP044135 SRS654977 GSM1429273 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429273 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429273 gds 301429273 GEO Accession GSM1429273 SRX647693 GSM1429274 SRP044135 SRS654976 GSM1429274 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429274 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429274 gds 301429274 GEO Accession GSM1429274 SRX647694 GSM1429275 SRP044135 SRS654978 GSM1429275 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429275 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429275 gds 301429275 GEO Accession GSM1429275 SRX647695 GSM1429276 SRP044135 SRS654979 GSM1429276 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429276 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429276 gds 301429276 GEO Accession GSM1429276 SRX647696 GSM1429277 SRP044135 SRS654980 GSM1429277 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429277 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429277 gds 301429277 GEO Accession GSM1429277 SRX647697 GSM1429278 SRP044135 SRS654981 GSM1429278 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429278 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429278 gds 301429278 GEO Accession GSM1429278 SRX647698 GSM1429279 SRP044135 SRS654982 GSM1429279 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429279 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429279 gds 301429279 GEO Accession GSM1429279 SRX647699 GSM1429280 SRP044135 SRS654984 GSM1429280 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429280 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429280 gds 301429280 GEO Accession GSM1429280 SRX647700 GSM1429281 SRP044135 SRS654983 GSM1429281 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429281 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429281 gds 301429281 GEO Accession GSM1429281 SRX647701 GSM1429282 SRP044135 SRS654985 GSM1429282 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429282 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429282 gds 301429282 GEO Accession GSM1429282 SRX647702 GSM1429283 SRP044135 SRS654986 GSM1429283 RNA-Seq TRANSCRIPTOMIC cDNA The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells. The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech). The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). 1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme). Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research). The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols. Illumina HiSeq 2000 GEO Sample GSM1429283 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429283 gds 301429283 GEO Accession GSM1429283