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Series GSE115746 Query DataSets for GSE115746
Status Public on Oct 31, 2018
Title Shared and distinct transcriptomic cell types across neocortical areas
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Neocortex contains a multitude of cell types segregated into layers and functionally distinct regions. To investigate the diversity of cell types across the mouse neocortex, we analyzed 12,714 cells from the primary visual cortex (VISp), and 9,035 cells from the anterior lateral motor cortex (ALM) by deep single-cell RNA-sequencing (scRNA-seq), identifying 116 transcriptomic cell types. These two regions represent distant poles of the neocortex and perform distinct functions. We define 50 inhibitory transcriptomic cell types, all of which are shared across both cortical regions. In contrast, 49 of 52 excitatory transcriptomic types were found in either VISp or ALM, with only three present in both. By combining single cell RNA-seq and retrograde labeling, we demonstrate correspondence between excitatory transcriptomic types and their region-specific long-range target specificity. This study establishes a combined transcriptomic and projectional taxonomy of cortical cell types from functionally distinct regions of the mouse cortex.
 
Overall design scRNA-seq of 25,481 single cells from two regions of adult Mouse cortex: anterior lateral motor cortex (ALM) and primary visual cortex (VISp) and 2,986 control samples

Please note that the current records represent 232-grouped sample records (i.e. 28706-samples collaped into 232-logical groups) and the complete metadata for each single sample is provided as 'complete_metadata_28706-cells.csv'.

The file 'accession_table.csv' provides all of the GEO and SRA IDs along with the sample_name/title that matches the metadata.
 
Contributor(s) Tasic B, Yao Z, Smith KA, Graybuck LT, Nguyen TN, Bertagnolli D, Goldy J, Garren E, Economo M, Viswanathan S, Penn O, Bakken T, Miller JA, Fong O, Hirokawa KE, Lathia K, Rimorin C, Tieu M, Larsen R, Casper T, Barkan E, Kroll M, Parry S, Shapovalova NV, Hirchstein D, Pendergraft J, Kim TK, Szafer A, Dee N, Groblewski P, Wickersham I, Cetin A, Harris JA, Levi BP, Sunkin SM, Madisen L, Daigle TL, Looger L, Bernard A, Phillips J, Lein E, Hawrylycz M, Svoboda K, Jones AR, Koch C, Zeng H
Citation(s) 30382198
Submission date Jun 13, 2018
Last update date Mar 21, 2019
Contact name Allen Institute
Organization name The Allen Institute for Brain Science
Street address 615 Westlake Ave N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (140)
GSM3189842 ALM_Ai14(RCL-tdT)/Ai14(RCL-tdT)_Retrograde_1
GSM3189843 ALM_Ai14(RCL-tdT)/Ai14(RCL-tdT)_Retrograde_2
GSM3189844 ALM_Ai14(RCL-tdT)/Ai14(RCL-tdT)_Retrograde_3
Relations
BioProject PRJNA476008
SRA SRP150473

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE115746_accession_table.csv.gz 173.6 Kb (ftp)(http) CSV
GSE115746_cells_exon_counts.csv.gz 319.2 Mb (ftp)(http) CSV
GSE115746_cells_intron_counts.csv.gz 155.0 Mb (ftp)(http) CSV
GSE115746_complete_metadata_28706-cells.csv.gz 489.9 Kb (ftp)(http) CSV
GSE115746_controls_exon_counts.csv.gz 21.5 Mb (ftp)(http) CSV
GSE115746_controls_intron_counts.csv.gz 14.0 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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