NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4987000 Query DataSets for GSM4987000
Status Public on Oct 07, 2021
Title IF1
Sample type SRA
 
Source name visual cortex
Organism Mus musculus
Characteristics strain: C57BL/6J 
age: post natal day 14
Sex: male
genotype: VGlut2 f/f
Growth protocol 12 hour light/dark cycle with ad lib access to standard mouse chow
Extracted molecule total RNA
Extraction protocol mice anesthetized with Ketamine/ Xylazine injection, then brain microdissection in cold PBS, snap freeze in ethanol+CO2. stored at -80C until use. On day of experiment, tissue digested to release single nucleus suspension, then immunostained against Neun, and FACS sorted to obtain Neun negative nuclei. Immediately proceeded to 10x chromium protocol, barcoding and cDNA preparation. cDNA stored at -30C until all samples collected. Libraries prepared from all samples at the same time.
10X chromium kit following manufacturer's instructions
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description from single nucleus barcode
Data processing BCL files from sequencer were demultiplexed by cellranger "mkfastq" function (v3.1.0)
Resulting FASTQ files were mapped by cellranger "count" function to mouse mm10 genome with gene annotations that came with cellranger to get the BAM file.
Genome_build: mm10
 
Submission date Dec 23, 2020
Last update date Oct 07, 2021
Contact name Nicola Allen
Organization name Salk Institute
Street address 10010 North Torrey Pines Rd
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL24247
Series (1)
GSE163775 Activity-dependent modulation of synapse-regulating genes in astrocytes
Relations
BioSample SAMN17147679
SRA SRX9724367

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap