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Sample GSM3615040 Query DataSets for GSM3615040
Status Public on Feb 21, 2019
Title BNST_Male_8c
Sample type SRA
 
Source name Bed nucleus of the stria terminalis
Organism Mus musculus
Characteristics strain: C57BL/6J
Sex: Male
tissue: Bed nucleus of the stria terminalis
Extracted molecule polyA RNA
Extraction protocol Perfused frozen tissues were finely minced and dissociated in an extraction media a based on that of Carter et al. 2009 with 0.1% Triton for 10 minutes. Extracted nuclei were washed in 30 mLs of media based on that of Carter et al. 2009 and pelleted by bucket centrifuge. Nuclei were filtered through a 40 um FlowMi filter before FACS sorting for singlets using a DAPI signal.
10X Chromium Single Cell 3' (V2 or V3) (manufacturer's protocol). Mouse: V3, human: V2.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Male8_BNST
single-nuclei gene expression data
BNST_region_neur_Mal_matrix.mtx
BNST_region_neur_Mal_barcodes.csv
BNST_region_neur_Mal_genes.csv
BNST_only_Mal_matrix.mtx
BNST_only_Mal_barcodes.csv
BNST_only_Mal_genes.csv
Data processing Genome_build: mm10_premrna
Mouse: R1:28 bp, R2:91 bp
Sequencing reads were demultiplexed and aligned against the mm10_premrna mouse genome build for BNST samples using 10x Cell Ranger v3.0.2; sequencing reads were demultiplexed and aligned against the GRCh38_premrna build for SN samples using 10x Cell Ranger v2.2
Digital gene expression matrices (with gene expression counts) were generated by Cell Ranger software (v3.0.2 for BNST samples, v2.2 for SN samples)
Digital gene expression matrices were analyzed and subset to specific regions using LIGER (v0.3)
Supplementary_files_format_and_content:
digital gene expression matrix (sparse format): matrix market format, rows = genes/transcripts, columns = barcodes/cells
barcodes list: names of barcodes/cells for corresponding DGE matrix file
genes list: names of transcripts/genes for corresponding DGE matrix file
BNST_only: nuclei determined to be neurons localized specifically to BNST
BNST_region_neur: nuclei determined to be neurons localized to the larger BNST region
 
Submission date Feb 20, 2019
Last update date Feb 21, 2019
Contact name Evan Macosko
E-mail(s) emacosko@broadinstitute.org
Organization name Broad Institute
Street address 75 Ames St, Broad Institute
City Cambridge
State/province Ma
ZIP/Postal code 02142
Country USA
 
Platform ID GPL24247
Series (1)
GSE126836 Single-cell multi-omic integration compares and contrasts features of brain cell identity
Relations
BioSample SAMN10977181
SRA SRX5399173

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

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