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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jul 15, 2016 |
Title |
1g_BTN3_C24_IL3971-707-502_CTCTCTAC-CTCTCTAT BTN03 Mic-scRNA-Seq |
Sample type |
SRA |
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Source name |
striatum
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Organism |
Mus musculus |
Characteristics |
experiment: BTN03 major cell type: Astro protocol: Mic-scRNA-Seq
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Extracted molecule |
polyA RNA |
Extraction protocol |
Acute brain slices were cut from 5-7 weeks old male mouse and after papain treatment dissociated mechanically (SI Methods). Live cells were purified by either magnetic bead-activated cell sorting (MACS;Miltenyi Biotec) or by fluorescence-activated cell sorting (FACS). For cell type specific isolation genetically labeled MSN subtypes D1-, D2-MSN, and astrocytes were purified by FACS. Single cells were captured on a microfluidic chip on the C1 system (Fluidigm) and whole-transcriptome amplified cDNA was prepared on chip using theSMARTer Ultra LowRNAkit for Illumina (Clontech). For smart-seq2 protocol, three MSN populations (D1-MSN tdTom+, D1-MSN GFP+ and tdTom+/GFP+ MSNs) sorted individually into 96 well plates with lysis buffer and spun down and frozen at -80°C and amplified using the protocol as described previously (Picelli et al., 2013). Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
polyA RNA Mic-scRNA-Seq
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Data processing |
Aligned using STAR Genes which overlapped with intergenic regions, introns, or multiples genes removed Number of reads aligning to each gene counted Genome_build: mm10 Supplementary_files_format_and_content: matrix, samples as rows and genes as columns. data is is log10(counts per million reads)
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Submission date |
Jun 06, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Stephen Quake |
E-mail(s) |
quake@stanford.edu
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Organization name |
Stanford Department of Bioengineering
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Street address |
450 Serra Mall
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City |
Stanford |
State/province |
CA |
ZIP/Postal code |
94305 |
Country |
USA |
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Platform ID |
GPL13112 |
Series (1) |
GSE82187 |
Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNAseq |
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Relations |
BioSample |
SAMN05211136 |
SRA |
SRX1826554 |
Supplementary data files not provided |
SRA Run Selector |
Processed data are available on Series record |
Raw data are available in SRA |
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