SRX3206574 GSM2790903 SRP118738 SRS2532390 GSM2790903 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790903 GSM2790903 GEO Accession GSM2790903 SRX3206575 GSM2790904 SRP118738 SRS2532391 GSM2790904 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790904 GSM2790904 GEO Accession GSM2790904 SRX3206576 GSM2790905 SRP118738 SRS2532392 GSM2790905 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790905 GSM2790905 GEO Accession GSM2790905 SRX3206577 GSM2790906 SRP118738 SRS2532393 GSM2790906 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790906 GSM2790906 GEO Accession GSM2790906 SRX3206578 GSM2790907 SRP118738 SRS2532394 GSM2790907 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790907 GSM2790907 GEO Accession GSM2790907 SRX3206579 GSM2790908 SRP118738 SRS2532395 GSM2790908 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790908 GSM2790908 GEO Accession GSM2790908 SRX3206580 GSM2790909 SRP118738 SRS2532397 GSM2790909 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790909 GSM2790909 GEO Accession GSM2790909 SRX3206581 GSM2790910 SRP118738 SRS2532396 GSM2790910 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790910 GSM2790910 GEO Accession GSM2790910 SRX3206582 GSM2790911 SRP118738 SRS2532398 GSM2790911 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790911 GSM2790911 GEO Accession GSM2790911 SRX3206583 GSM2790912 SRP118738 SRS2532399 GSM2790912 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790912 GSM2790912 GEO Accession GSM2790912 SRX3206584 GSM2790913 SRP118738 SRS2532400 GSM2790913 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790913 GSM2790913 GEO Accession GSM2790913 SRX3206585 GSM2790914 SRP118738 SRS2532401 GSM2790914 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790914 GSM2790914 GEO Accession GSM2790914 SRX3206586 GSM2790915 SRP118738 SRS2532403 GSM2790915 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790915 GSM2790915 GEO Accession GSM2790915 SRX3206587 GSM2790916 SRP118738 SRS2532402 GSM2790916 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790916 GSM2790916 GEO Accession GSM2790916 SRX3206588 GSM2790917 SRP118738 SRS2532404 GSM2790917 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790917 GSM2790917 GEO Accession GSM2790917 SRX3206589 GSM2790918 SRP118738 SRS2532405 GSM2790918 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790918 GSM2790918 GEO Accession GSM2790918 SRX3206590 GSM2790919 SRP118738 SRS2532406 GSM2790919 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790919 GSM2790919 GEO Accession GSM2790919 SRX3206591 GSM2790920 SRP118738 SRS2532407 GSM2790920 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790920 GSM2790920 GEO Accession GSM2790920 SRX3206592 GSM2790921 SRP118738 SRS2532409 GSM2790921 RNA-Seq TRANSCRIPTOMIC cDNA After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection. Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500. Illumina HiSeq 2500 gds 302790921 GSM2790921 GEO Accession GSM2790921