NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3061560 Query DataSets for GSM3061560
Status Public on Feb 13, 2019
Title Th17 + CB839 3
Sample type SRA
 
Source name Th17 cells
Organism Mus musculus
Characteristics agent: CB839
cell type: Th17 cells
Treatment protocol Cells were treated with glutaminase1 inhibitor or vehicle
Growth protocol Primary mouse CD4+ T cells differentiated over 5 days with subset-specific cytokines and growth cytokine IL-2
Extracted molecule total RNA
Extraction protocol CD4+ T cells isolated after treatment and total RNA extracted
At least 100ng of DNase-treated total RNA was used to generate polyA-enriched mRNA libraries using NEBNext polyA mRNA sample kits with indexed adaptors (New England Biolabs). Library quality was assessed using the 2100 Bioanalyzer (Agilent) and libraries were quantitated using KAPA Library Quantification Kits (Roche).
Pooled libraries were subjected to 75 bp paired-end sequencing according to the manufacturer’s protocol (Illumina HiSeq3000). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description Sample.12
Data processing Sequencing reads were aligned against the Mouse GENCODE genome, Version M14 (January 2017 freeze, GRCm38, Ensembl 89) using the Spliced Transcripts Alignment to a Reference (STAR) software (PMID: 26187010 and 23104886).
Reads were preprocessed and index using SAMtools (PMID: 19505943).
Mapped reads were assigned to gene features and quantified using featureCounts (PMID: 24227677).
Raw counts where read into R, and normalized using DESeq2 (PMID: 25516281) with the variance stabilizing normalization function.
Genome_build: Mouse GENCODE genome, Version M14 (January 2017 freeze, GRCm38, Ensembl 89)
Supplementary_files_format_and_content: Raw Counts
 
Submission date Mar 23, 2018
Last update date Feb 13, 2019
Contact name Aguirre A de Cubas
E-mail(s) a.decubas@vumc.org
Organization name Vanderbilt University Medical Center
Department Hematology and Oncology
Lab Rathmell Lab
Street address 2220 Pierce Ave
City NASHVILLE
State/province TN
ZIP/Postal code 37232
Country USA
 
Platform ID GPL21493
Series (1)
GSE112244 Th1 and T17 activation with and without CB839 treatment
Relations
BioSample SAMN08782054
SRA SRX3835396

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