SRX255934 RL2011_11 SRP020097 PRJNA194438 NPCs were grown and harvested, as for passaging, and kept on ice in Hank’s balanced salt solution (HBSS, Gibco). One-third of this population was used for whole cell micromanipulation or sorting. Whole cells reporting EYFP expression were chosen for downstream micromanipulation and cDNA synthesis. The rest (two-thirds) was transferred to nuclei isolation media [(NIM) 250mM sucrose, 25mM KCl, 5mM MgCl2, 10 mM Tris], aspirated three times through a 27 g needle, and centrifuged at 1,200 X g for 8 minutes to obtain a crude nuclei prep. Nuclei were further purified using a iodixanol cushion and centrifuged at 10300 X g for 20 minutes. An aliquot of the purified nuclei was observed by fluorescence microscopy to confirm the absence of the EYFP signal. A candidate single cell or nucleus was selected from the population and serially washed in cold phosphate buffered saline (PBS) to remove potential nucleic acid contaminants from the sample. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides. SRS405334 SAMN01993129 RL2011_11 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System SRX255935 RL2011_12 SRP020097 NPCs were grown and harvested, as for passaging, and kept on ice in Hank’s balanced salt solution (HBSS, Gibco). One-third of this population was used for whole cell micromanipulation or sorting. Whole cells reporting EYFP expression were chosen for downstream micromanipulation and cDNA synthesis. The rest (two-thirds) was transferred to nuclei isolation media [(NIM) 250mM sucrose, 25mM KCl, 5mM MgCl2, 10 mM Tris], aspirated three times through a 27 g needle, and centrifuged at 1,200 X g for 8 minutes to obtain a crude nuclei prep. Nuclei were further purified using a iodixanol cushion and centrifuged at 10300 X g for 20 minutes. An aliquot of the purified nuclei was observed by fluorescence microscopy to confirm the absence of the EYFP signal. A candidate single cell or nucleus was selected from the population and serially washed in cold phosphate buffered saline (PBS) to remove potential nucleic acid contaminants from the sample. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides. SRS405334 mouseNPC RL2011_12 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System SRX255938 RL2011_13 SRP020097 NPCs were grown and harvested, as for passaging, and kept on ice in Hank’s balanced salt solution (HBSS, Gibco). One-third of this population was used for whole cell micromanipulation or sorting. Whole cells reporting EYFP expression were chosen for downstream micromanipulation and cDNA synthesis. The rest (two-thirds) was transferred to nuclei isolation media [(NIM) 250mM sucrose, 25mM KCl, 5mM MgCl2, 10 mM Tris], aspirated three times through a 27 g needle, and centrifuged at 1,200 X g for 8 minutes to obtain a crude nuclei prep. Nuclei were further purified using a iodixanol cushion and centrifuged at 10300 X g for 20 minutes. An aliquot of the purified nuclei was observed by fluorescence microscopy to confirm the absence of the EYFP signal. A candidate single cell or nucleus was selected from the population and serially washed in cold phosphate buffered saline (PBS) to remove potential nucleic acid contaminants from the sample. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides. SRS405334 mouseNPC RL2011_13 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System SRX256509 JY-101211-9 SRP020097 Prox1-GFP mice were anesthetized with a ketamine/xylazine mixture and transcardially perfused with 0.9% NaCl solution followed by 4% paraformaldehyde (PFA) in 0.1 M phosphate buffer, pH 7.4. Brain tissue was postfixed overnight in 4% PFA at 40C and then transferred into a 30% sucrose solution. 40 μm coronal sections were cut on a sliding microtome and all immunohistochemistry was performed on free-floating sections. Tissue from animals was incubated with an antibody against Prox-1 for 48 h at 40C followed by incubation with a secondary antibody. The primary antibody was rabbit anti-Prox1 (1:250, Covance). Images were taken using a confocal microscope (Radiance 2100; Bio-Rad, Hercules, CA). A transgenic mouse expressing GFP under the Prox1 promoter enabled the observation of endogenous Prox1 expression in vivo. The DG was isolated by dissection as before(Lein et al. 2004). Nuclei were obtained from freshly dissected tissue using a polytron (Kinematica, Inc. Bohemia, NY) followed by dounce homogenization in NIM + 0.5% triton. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides SRS404734 MusProx1-GFP JY-101211-9 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD System 3.0 SRX256510 JY-101211-10 SRP020097 Prox1-GFP mice were anesthetized with a ketamine/xylazine mixture and transcardially perfused with 0.9% NaCl solution followed by 4% paraformaldehyde (PFA) in 0.1 M phosphate buffer, pH 7.4. Brain tissue was postfixed overnight in 4% PFA at 40C and then transferred into a 30% sucrose solution. 40 μm coronal sections were cut on a sliding microtome and all immunohistochemistry was performed on free-floating sections. Tissue from animals was incubated with an antibody against Prox-1 for 48 h at 40C followed by incubation with a secondary antibody. The primary antibody was rabbit anti-Prox1 (1:250, Covance). Images were taken using a confocal microscope (Radiance 2100; Bio-Rad, Hercules, CA). A transgenic mouse expressing GFP under the Prox1 promoter enabled the observation of endogenous Prox1 expression in vivo. The DG was isolated by dissection as before(Lein et al. 2004). Nuclei were obtained from freshly dissected tissue using a polytron (Kinematica, Inc. Bohemia, NY) followed by dounce homogenization in NIM + 0.5% triton. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides SRS404734 MusProx1-GFP JY-101211-10 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD System 3.0 SRX256516 JY-101211-8 SRP020097 Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides SRS255193 C57BL/6J JY-101211-8 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System SRX256805 RL2011_14 SRP020097 NPCs were grown and harvested, as for passaging, and kept on ice in Hank’s balanced salt solution (HBSS, Gibco). One-third of this population was used for whole cell micromanipulation or sorting. Whole cells reporting EYFP expression were chosen for downstream micromanipulation and cDNA synthesis. The rest (two-thirds) was transferred to nuclei isolation media [(NIM) 250mM sucrose, 25mM KCl, 5mM MgCl2, 10 mM Tris], aspirated three times through a 27 g needle, and centrifuged at 1,200 X g for 8 minutes to obtain a crude nuclei prep. Nuclei were further purified using a iodixanol cushion and centrifuged at 10300 X g for 20 minutes. An aliquot of the purified nuclei was observed by fluorescence microscopy to confirm the absence of the EYFP signal. A candidate single cell or nucleus was selected from the population and serially washed in cold phosphate buffered saline (PBS) to remove potential nucleic acid contaminants from the sample. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides. SRS405334 mouseNPC RL2011_14 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System SRX256806 RL2011_15 SRP020097 NPCs were grown and harvested, as for passaging, and kept on ice in Hank’s balanced salt solution (HBSS, Gibco). One-third of this population was used for whole cell micromanipulation or sorting. Whole cells reporting EYFP expression were chosen for downstream micromanipulation and cDNA synthesis. The rest (two-thirds) was transferred to nuclei isolation media [(NIM) 250mM sucrose, 25mM KCl, 5mM MgCl2, 10 mM Tris], aspirated three times through a 27 g needle, and centrifuged at 1,200 X g for 8 minutes to obtain a crude nuclei prep. Nuclei were further purified using a iodixanol cushion and centrifuged at 10300 X g for 20 minutes. An aliquot of the purified nuclei was observed by fluorescence microscopy to confirm the absence of the EYFP signal. A candidate single cell or nucleus was selected from the population and serially washed in cold phosphate buffered saline (PBS) to remove potential nucleic acid contaminants from the sample. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides. SRS405334 mouseNPC RL2011_15 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System SRX256809 RL2011_16 SRP020097 NPCs were grown and harvested, as for passaging, and kept on ice in Hank’s balanced salt solution (HBSS, Gibco). One-third of this population was used for whole cell micromanipulation or sorting. Whole cells reporting EYFP expression were chosen for downstream micromanipulation and cDNA synthesis. The rest (two-thirds) was transferred to nuclei isolation media [(NIM) 250mM sucrose, 25mM KCl, 5mM MgCl2, 10 mM Tris], aspirated three times through a 27 g needle, and centrifuged at 1,200 X g for 8 minutes to obtain a crude nuclei prep. Nuclei were further purified using a iodixanol cushion and centrifuged at 10300 X g for 20 minutes. An aliquot of the purified nuclei was observed by fluorescence microscopy to confirm the absence of the EYFP signal. A candidate single cell or nucleus was selected from the population and serially washed in cold phosphate buffered saline (PBS) to remove potential nucleic acid contaminants from the sample. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides. SRS405334 mouseNPC RL2011_16 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System SRX256810 RL2011_17 SRP020097 NPCs were grown and harvested, as for passaging, and kept on ice in Hank’s balanced salt solution (HBSS, Gibco). One-third of this population was used for whole cell micromanipulation or sorting. Whole cells reporting EYFP expression were chosen for downstream micromanipulation and cDNA synthesis. The rest (two-thirds) was transferred to nuclei isolation media [(NIM) 250mM sucrose, 25mM KCl, 5mM MgCl2, 10 mM Tris], aspirated three times through a 27 g needle, and centrifuged at 1,200 X g for 8 minutes to obtain a crude nuclei prep. Nuclei were further purified using a iodixanol cushion and centrifuged at 10300 X g for 20 minutes. An aliquot of the purified nuclei was observed by fluorescence microscopy to confirm the absence of the EYFP signal. A candidate single cell or nucleus was selected from the population and serially washed in cold phosphate buffered saline (PBS) to remove potential nucleic acid contaminants from the sample. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides. SRS405334 mouseNPC RL2011_17 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System SRX256811 RL2011_18 SRP020097 NPCs were grown and harvested, as for passaging, and kept on ice in Hank’s balanced salt solution (HBSS, Gibco). One-third of this population was used for whole cell micromanipulation or sorting. Whole cells reporting EYFP expression were chosen for downstream micromanipulation and cDNA synthesis. The rest (two-thirds) was transferred to nuclei isolation media [(NIM) 250mM sucrose, 25mM KCl, 5mM MgCl2, 10 mM Tris], aspirated three times through a 27 g needle, and centrifuged at 1,200 X g for 8 minutes to obtain a crude nuclei prep. Nuclei were further purified using a iodixanol cushion and centrifuged at 10300 X g for 20 minutes. An aliquot of the purified nuclei was observed by fluorescence microscopy to confirm the absence of the EYFP signal. A candidate single cell or nucleus was selected from the population and serially washed in cold phosphate buffered saline (PBS) to remove potential nucleic acid contaminants from the sample. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides. SRS405334 mouseNPC RL2011_18 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System SRX256812 RL2011_19 SRP020097 NPCs were grown and harvested, as for passaging, and kept on ice in Hank’s balanced salt solution (HBSS, Gibco). One-third of this population was used for whole cell micromanipulation or sorting. Whole cells reporting EYFP expression were chosen for downstream micromanipulation and cDNA synthesis. The rest (two-thirds) was transferred to nuclei isolation media [(NIM) 250mM sucrose, 25mM KCl, 5mM MgCl2, 10 mM Tris], aspirated three times through a 27 g needle, and centrifuged at 1,200 X g for 8 minutes to obtain a crude nuclei prep. Nuclei were further purified using a iodixanol cushion and centrifuged at 10300 X g for 20 minutes. An aliquot of the purified nuclei was observed by fluorescence microscopy to confirm the absence of the EYFP signal. A candidate single cell or nucleus was selected from the population and serially washed in cold phosphate buffered saline (PBS) to remove potential nucleic acid contaminants from the sample. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides. SRS405334 mouseNPC RL2011_19 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System SRX256825 RL2011_20 SRP020097 NPCs were grown and harvested, as for passaging, and kept on ice in Hank’s balanced salt solution (HBSS, Gibco). One-third of this population was used for whole cell micromanipulation or sorting. Whole cells reporting EYFP expression were chosen for downstream micromanipulation and cDNA synthesis. The rest (two-thirds) was transferred to nuclei isolation media [(NIM) 250mM sucrose, 25mM KCl, 5mM MgCl2, 10 mM Tris], aspirated three times through a 27 g needle, and centrifuged at 1,200 X g for 8 minutes to obtain a crude nuclei prep. Nuclei were further purified using a iodixanol cushion and centrifuged at 10300 X g for 20 minutes. An aliquot of the purified nuclei was observed by fluorescence microscopy to confirm the absence of the EYFP signal. A candidate single cell or nucleus was selected from the population and serially washed in cold phosphate buffered saline (PBS) to remove potential nucleic acid contaminants from the sample. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides. SRS405334 mouseNPC RL2011_20 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System SRX256826 RL2011_21 SRP020097 NPCs were grown and harvested, as for passaging, and kept on ice in Hank’s balanced salt solution (HBSS, Gibco). One-third of this population was used for whole cell micromanipulation or sorting. Whole cells reporting EYFP expression were chosen for downstream micromanipulation and cDNA synthesis. The rest (two-thirds) was transferred to nuclei isolation media [(NIM) 250mM sucrose, 25mM KCl, 5mM MgCl2, 10 mM Tris], aspirated three times through a 27 g needle, and centrifuged at 1,200 X g for 8 minutes to obtain a crude nuclei prep. Nuclei were further purified using a iodixanol cushion and centrifuged at 10300 X g for 20 minutes. An aliquot of the purified nuclei was observed by fluorescence microscopy to confirm the absence of the EYFP signal. A candidate single cell or nucleus was selected from the population and serially washed in cold phosphate buffered saline (PBS) to remove potential nucleic acid contaminants from the sample. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides. SRS405334 mouseNPC RL2011_21 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System SRX256827 RL2011_22 SRP020097 NPCs were grown and harvested, as for passaging, and kept on ice in Hank’s balanced salt solution (HBSS, Gibco). One-third of this population was used for whole cell micromanipulation or sorting. Whole cells reporting EYFP expression were chosen for downstream micromanipulation and cDNA synthesis. The rest (two-thirds) was transferred to nuclei isolation media [(NIM) 250mM sucrose, 25mM KCl, 5mM MgCl2, 10 mM Tris], aspirated three times through a 27 g needle, and centrifuged at 1,200 X g for 8 minutes to obtain a crude nuclei prep. Nuclei were further purified using a iodixanol cushion and centrifuged at 10300 X g for 20 minutes. An aliquot of the purified nuclei was observed by fluorescence microscopy to confirm the absence of the EYFP signal. A candidate single cell or nucleus was selected from the population and serially washed in cold phosphate buffered saline (PBS) to remove potential nucleic acid contaminants from the sample. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides. SRS405334 mouseNPC RL2011_22 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System SRX256828 RL2011_23 SRP020097 NPCs were grown and harvested, as for passaging, and kept on ice in Hank’s balanced salt solution (HBSS, Gibco). One-third of this population was used for whole cell micromanipulation or sorting. Whole cells reporting EYFP expression were chosen for downstream micromanipulation and cDNA synthesis. The rest (two-thirds) was transferred to nuclei isolation media [(NIM) 250mM sucrose, 25mM KCl, 5mM MgCl2, 10 mM Tris], aspirated three times through a 27 g needle, and centrifuged at 1,200 X g for 8 minutes to obtain a crude nuclei prep. Nuclei were further purified using a iodixanol cushion and centrifuged at 10300 X g for 20 minutes. An aliquot of the purified nuclei was observed by fluorescence microscopy to confirm the absence of the EYFP signal. A candidate single cell or nucleus was selected from the population and serially washed in cold phosphate buffered saline (PBS) to remove potential nucleic acid contaminants from the sample. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides. SRS405334 mouseNPC RL2011_23 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System SRX256829 RL2011_24 SRP020097 NPCs were grown and harvested, as for passaging, and kept on ice in Hank’s balanced salt solution (HBSS, Gibco). One-third of this population was used for whole cell micromanipulation or sorting. Whole cells reporting EYFP expression were chosen for downstream micromanipulation and cDNA synthesis. The rest (two-thirds) was transferred to nuclei isolation media [(NIM) 250mM sucrose, 25mM KCl, 5mM MgCl2, 10 mM Tris], aspirated three times through a 27 g needle, and centrifuged at 1,200 X g for 8 minutes to obtain a crude nuclei prep. Nuclei were further purified using a iodixanol cushion and centrifuged at 10300 X g for 20 minutes. An aliquot of the purified nuclei was observed by fluorescence microscopy to confirm the absence of the EYFP signal. A candidate single cell or nucleus was selected from the population and serially washed in cold phosphate buffered saline (PBS) to remove potential nucleic acid contaminants from the sample. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides. SRS405334 mouseNPC RL2011_24 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System SRX256832 RL2011_25 SRP020097 NPCs were grown and harvested, as for passaging, and kept on ice in Hank’s balanced salt solution (HBSS, Gibco). One-third of this population was used for whole cell micromanipulation or sorting. Whole cells reporting EYFP expression were chosen for downstream micromanipulation and cDNA synthesis. The rest (two-thirds) was transferred to nuclei isolation media [(NIM) 250mM sucrose, 25mM KCl, 5mM MgCl2, 10 mM Tris], aspirated three times through a 27 g needle, and centrifuged at 1,200 X g for 8 minutes to obtain a crude nuclei prep. Nuclei were further purified using a iodixanol cushion and centrifuged at 10300 X g for 20 minutes. An aliquot of the purified nuclei was observed by fluorescence microscopy to confirm the absence of the EYFP signal. A candidate single cell or nucleus was selected from the population and serially washed in cold phosphate buffered saline (PBS) to remove potential nucleic acid contaminants from the sample. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides. SRS405334 mouseNPC RL2011_25 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System SRX256833 RL2011_26 SRP020097 NPCs were grown and harvested, as for passaging, and kept on ice in Hank’s balanced salt solution (HBSS, Gibco). One-third of this population was used for whole cell micromanipulation or sorting. Whole cells reporting EYFP expression were chosen for downstream micromanipulation and cDNA synthesis. The rest (two-thirds) was transferred to nuclei isolation media [(NIM) 250mM sucrose, 25mM KCl, 5mM MgCl2, 10 mM Tris], aspirated three times through a 27 g needle, and centrifuged at 1,200 X g for 8 minutes to obtain a crude nuclei prep. Nuclei were further purified using a iodixanol cushion and centrifuged at 10300 X g for 20 minutes. An aliquot of the purified nuclei was observed by fluorescence microscopy to confirm the absence of the EYFP signal. A candidate single cell or nucleus was selected from the population and serially washed in cold phosphate buffered saline (PBS) to remove potential nucleic acid contaminants from the sample. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides. SRS405334 mouseNPC RL2011_26 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System SRX256834 RL2011_27 SRP020097 NPCs were grown and harvested, as for passaging, and kept on ice in Hank’s balanced salt solution (HBSS, Gibco). One-third of this population was used for whole cell micromanipulation or sorting. Whole cells reporting EYFP expression were chosen for downstream micromanipulation and cDNA synthesis. The rest (two-thirds) was transferred to nuclei isolation media [(NIM) 250mM sucrose, 25mM KCl, 5mM MgCl2, 10 mM Tris], aspirated three times through a 27 g needle, and centrifuged at 1,200 X g for 8 minutes to obtain a crude nuclei prep. Nuclei were further purified using a iodixanol cushion and centrifuged at 10300 X g for 20 minutes. An aliquot of the purified nuclei was observed by fluorescence microscopy to confirm the absence of the EYFP signal. A candidate single cell or nucleus was selected from the population and serially washed in cold phosphate buffered saline (PBS) to remove potential nucleic acid contaminants from the sample. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides. SRS405334 mouseNPC RL2011_27 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System SRX256835 RL2011_28 SRP020097 NPCs were grown and harvested, as for passaging, and kept on ice in Hank’s balanced salt solution (HBSS, Gibco). One-third of this population was used for whole cell micromanipulation or sorting. Whole cells reporting EYFP expression were chosen for downstream micromanipulation and cDNA synthesis. The rest (two-thirds) was transferred to nuclei isolation media [(NIM) 250mM sucrose, 25mM KCl, 5mM MgCl2, 10 mM Tris], aspirated three times through a 27 g needle, and centrifuged at 1,200 X g for 8 minutes to obtain a crude nuclei prep. Nuclei were further purified using a iodixanol cushion and centrifuged at 10300 X g for 20 minutes. An aliquot of the purified nuclei was observed by fluorescence microscopy to confirm the absence of the EYFP signal. A candidate single cell or nucleus was selected from the population and serially washed in cold phosphate buffered saline (PBS) to remove potential nucleic acid contaminants from the sample. Fragment libraries were constructed following published protocols for the SOLiD platform(Tang et al. 2010b). In a single-end, 50 base pair read run, multiplexed samples were sequenced on each of two slides. SRS405334 mouseNPC RL2011_28 RNA-Seq TRANSCRIPTOMIC RANDOM 50 0 Application Read Forward 1 AB SOLiD 4 System