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Sample GSM7290706 Query DataSets for GSM7290706
Status Public on Aug 07, 2023
Title HHV57DSXY_19005484_S64,TT4_A,WT_EFFECTOR
Sample type SRA
 
Source name EFFECTOR
Organism Mus musculus
Characteristics genotype: wildtype
cell type: EFFECTOR
Extracted molecule polyA RNA
Extraction protocol Poly-A selected RNA-seq libraries were constructed from 1 mg total RNA using the Illumina TruSeq RNA Sample Prep Kits, version 2. The resulting cDNA was fragmented using a Covaris E210. Library amplification was performed using 11 cycles to minimize the risk of over amplification. Unique barcode adapters were applied to each library. Libraries were quantitated by qPCR using the KAPA Library Quantification Kit (KAPA Biosystems) and pooled in an equimolar ratio. The pooled libraries were sequenced on a NovaSeq 6000 with version 1 chemistry. At least 90 million 150-base read pairs were generated for each individual library. Data was processed using RTA 3.4.4.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing RNA-seq data QC with QoRTs (version 1.3.6)
Sequence reads were aligned to mm10 with STAR (version 2.7.6a)
Transcript abundances from RNA-Seq data were quantified by usig RSEM (version 1.3.3)
Expected counts of the transcripts were then analyzed for differential expression with R package DESeq2
Assembly: mm10 (GRCm38.101)
Supplementary files format and content: tab-delimited text files
 
Submission date May 03, 2023
Last update date Aug 07, 2023
Contact name Peter McGuire
E-mail(s) peter.mcguire@nih.gov, payal.banerjee@nih.gov
Organization name NHGRI
Street address 10 Center Dr
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL24247
Series (2)
GSE231553 Pyruvate dehydrogenase complex integrates the metabolome and epigenome in memory CD8+ T cell differentiation in vitro [RNA-Seq]
GSE231556 Pyruvate dehydrogenase complex integrates the metabolome and epigenome in memory CD8+ T cell differentiation in vitro
Relations
BioSample SAMN34566579
SRA SRX20204035

Supplementary file Size Download File type/resource
GSM7290706_HHV57DSXY_19005484_S64.genes.results.gz 1.1 Mb (ftp)(http) RESULTS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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