NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2671346 Query DataSets for GSM2671346
Status Public on Jun 20, 2017
Title cgas_tp1.4
Sample type SRA
 
Source name cGAS KO MEFs d33
Organism Mus musculus
Characteristics strain: C57B1/6
genotype: cGAS KO
cell type: primary mouse embryonic fibroblast
passages: 11
Extracted molecule total RNA
Extraction protocol Total RNA from bulk MEF populations was extracted using the RNeasy mini kit (Qiagen). 1.5 and 3 ug of total RNA was used for the preparation of the library using the TruSeq mRNA stranded LT (Illumina kit)
TruSeq mRNA stranded LT (Illumina kit), with qubit quantification and QC with tapestation 4200 and Fragment analyzer.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description cGAS KO MEFs d33 rep4
Data processing Mapping: software Bowtie2 v.2.2.1, assembly: mm10
web-based HTSstation was used to process the data (David, et al. 2014)
RNA counter: HTSstation
Differential expression analysis: Bioconductor limma (v. 3.18.13)
Supplementary_files_format_and_content: tab-delimited text files include counts and RPKM values for each sample.
 
Submission date Jun 16, 2017
Last update date May 15, 2019
Contact name Selene Glück
E-mail(s) selene.glueck@epfl.ch
Organization name EPFL
Department SV-GHI
Lab Ablasser
Street address Station 19
City Lausanne
ZIP/Postal code 1015
Country Switzerland
 
Platform ID GPL19057
Series (1)
GSE100102 Innate immune sensing of cytosolic chromatin fragments through cGAS promotes senescence
Relations
BioSample SAMN07249236
SRA SRX2924833

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