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Series GSE82187 Query DataSets for GSE82187
Status Public on Jul 15, 2016
Title Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNAseq
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The striatum contributes to many cognitive processes and disorders, but its cell types are incompletely characterized. We show that microfluidic and FACS-based single-cell RNA sequencing of mouse striatum provides a well-resolved classification of striatal cell type diversity. Transcriptome analysis revealed 10 differentiated distinct cell types, including neurons, astrocytes, oligodendrocytes, ependymal, immune, and vascular cells, and enabled the discovery of numerous novel marker genes. Furthermore, we identified two discrete subtypes of medium spiny neurons (MSN) which have specific markers and which overexpress genes linked to cognitive disorders and addiction. We also describe continuous cellular identities, which increase heterogeneity within discrete cell types. Finally, we identified cell type specific transcription and splicing factors that shape cellular identities by regulating splicing and expression patterns. Our findings suggest that functional diversity within a complex tissue arises from a small number of discrete cell types, which can exist in a continuous spectrum of functional states.
 
Overall design We measured the transcriptome of 1208 single striatal cells using two complementary approaches; microfluidic single-cell RNAseq (Mic-scRNAseq) and single cell isolation by FACS (FACS-scRNAseq) (Table S1). We sampled cells either randomly or enriched specifically for MSNs or astrocytes using FACS from D1- tdTomato (tdTom)/D2-GFP or Aldhl1-GFP mice, respectively
 
Contributor(s) Stanley GM, Treutlein B, Quake SR
Citation(s) 27425622
Submission date Jun 02, 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
 
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (1208)
GSM2188962 1-0-0-0-BTN22-C34-8ul-1 BTN22 Mic-scRNA-Seq
GSM2188963 1-0-0-0-BTN24-C29-18ul-IL5195-708-502 BTN24 Mic-scRNA-Seq
GSM2188964 1-0-0-0-BTN24-C59-22ul-IL5195-710-505 BTN24 Mic-scRNA-Seq
Relations
BioProject PRJNA324641
SRA SRP076212

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MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE82187_cast_all_forGEO.csv.gz 20.8 Mb (ftp)(http) CSV
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Raw data are available in SRA
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