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Sample GSM2189356 Query DataSets for GSM2189356
Status Public on Jul 15, 2016
Title 1g_BTN3_C24_IL3971-707-502_CTCTCTAC-CTCTCTAT BTN03 Mic-scRNA-Seq
Sample type SRA
 
Source name striatum
Organism Mus musculus
Characteristics experiment: BTN03
major cell type: Astro
protocol: Mic-scRNA-Seq
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description polyA RNA Mic-scRNA-Seq
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)
 
Submission date Jun 06, 2016
Last update date May 15, 2019
Contact name Stephen Quake
E-mail(s) quake@stanford.edu
Organization name Stanford Department of Bioengineering
Street address 450 Serra Mall
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL13112
Series (1)
GSE82187 Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNAseq
Relations
BioSample SAMN05211136
SRA SRX1826554

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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