NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2967049 Query DataSets for GSM2967049
Status Public on Mar 19, 2018
Title Fat
Sample type SRA
 
Source name Fat
Organism Mus musculus
Characteristics tissue: Fat
age: 3 months
Extracted molecule total RNA
Extraction protocol single-cell sorting in 96-well plates followed by cDNA preparation using Smart-seq2
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT
Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description single cell
Data processing Sequences from the NovaSeq were demultiplexed using bcl2fastq version 2.19.0.316. Reads were aligned using to a copy of the mm10 genome augmented with ERCC sequences, using STAR version 2.5.2b
STAR options are listed below
--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMstrandField in
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated-value files with raw read counts for each sample
 
Submission date Jan 29, 2018
Last update date May 14, 2019
Contact name Angela Oliveira Pisco
E-mail(s) angela.pisco@czbiohub.org
Organization name CZ Biohub
Department Data Sciences
Street address 499 Illinois St
City San Francisco
State/province CA
ZIP/Postal code 94103
Country USA
 
Platform ID GPL24247
Series (2)
GSE109774 Tabula Muris: Transcriptomic characterization of 20 organs and tissues from Mus musculus at single cell resolution
GSE132042 Tabula Muris
Relations
BioSample SAMN08428466
SRA SRX3607045

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