|
| Status |
Public on Feb 21, 2019 |
| Title |
BNST_Female_4a |
| Sample type |
SRA |
| |
|
| Source name |
Bed nucleus of the stria terminalis
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
Sex: Female
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 |
Female4_BNST
single-nuclei gene expression data
BNST_region_neur_Fem_matrix.mtx
BNST_region_neur_Fem_barcodes.csv
BNST_region_neur_Fem_genes.csv
BNST_only_Fem_matrix.mtx
BNST_only_Fem_barcodes.csv
BNST_only_Fem_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 |
SAMN10977152 |
| SRA |
SRX5399202 |
