NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2247811 Query DataSets for GSM2247811
Status Public on Jul 04, 2018
Title DMSO treated Th1 cells Rep 2
Sample type SRA
 
Source name DMSO treated Th1 cells
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: In vitro IL12 differentiated Th1 cells
treatment: DMSO treated
Growth protocol T cells were purified and activated with plate-bound anti-Hamster IgG (MP Biomedicals) and anti-CD3 (2C11, Bio X cell) +anti-CD28 (37N, Bio X cell) in the presence of anti-IL-4 (5 _g/ml; 11B11) and IL-12 (2 ng/ml; PeproTech)
Extracted molecule polyA RNA
Extraction protocol Total RNA was isolated with RNeasy plus kit
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description CD4 T cells
processed data files: RNAseq_cpx_vs_dmso_DESeq2.txt, RPM.txt
Data processing Adaptors were first trimmed from the sequence reads with CUTADAPT
RNA seq reads were aligned to mm9 with STAR
The number of aligned reads that overlap each gene in the annotations (mm9) was counted with HTseq-count, and normalized gene expression (RPM) was determined by Deseq 2.
Differential gene expression was analyzed with Deseq
Genome_build: mm9
Supplementary_files_format_and_content: [.txt] tab-delimited text files include RPM values for each Sample and differential gene expression.
 
Submission date Jul 21, 2016
Last update date May 15, 2019
Contact name Xing Chang
E-mail(s) changxing@sibs.ac.cn
Organization name Shanghai Institute for Biological Sciences
Street address 320 Yueyang road
City Shanghai
ZIP/Postal code 200031
Country China
 
Platform ID GPL21273
Series (2)
GSE84699 Transcriptome targets of PCBP1 in T cells
GSE84702 Iron-mediated stabilization of PCBP1 post-transcriptionally promotes GM-CSF production during autoimmune pathogenesis
Relations
BioSample SAMN05427609
SRA SRX1969224

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