NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1120731 Query DataSets for GSM1120731
Status Public on Jun 27, 2013
Title mRNA-Th1
Sample type SRA
 
Source name primary CD4+ T cells from spleen and lymph nodes
Organism Mus musculus
Characteristics strain: C57BL/6J
genotype/variation: wild type
cell type: in vitro polarized T helper1 cells for 3 days
passages: FACS sorted naive CD4+T cells cultured in vitro for 3 days under Th1 condition
Growth protocol Control and Bach2-deficient naïve CD4+CD44-CD25-CD62L+ T cells were isolated and sorted on the flow cytometer. Cells were cultured with plate-bound anti-CD3 and anti-CD28 (10 ug/ml each)either under: Th1conditions (IL-12 (20 ng ml) and anti-IL-4 neutralizing antibodies (10 μgml-1); Th2 conditions (IL-4 (20 ng ml-1) and anti-IFN-γneutralizing antibodies (10 μg ml-1); Th17 conditions (IL-6 (20 ng ml-1) plus human TGF-β1 (2 ng ml-1) and anti-IFN-γ neutralizing antibodies (10 μg ml-1) and anti-IL-4 neutralizing antibodies (10 μg ml-1)) or iTreg conditions(IL-2 (100 IU ml-1) plus human TGF-β1 (5 ng ml-1) for 3 days.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from approximately 1 million cells by using mirVana miRNA Isolation Kit(AM1560, ABI). 200 ng of total RNA was subsequently used to prepare RNA-seq library byusing TruSeq SRRNA sample prep kit (FC-122-1001, Illumina) by following manufacturer’s protocol.The resulted libraries are sequenced using the Illumina HiSeq 2000. Only unique reads of 50 bp were mapped to the mouse genome (mm9) using Tophat and Cufflinks.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description mRNA_seq
RUN DATE: 7/6/2010
Data processing RNA-seq: Tophat and cufflinks. Sequence reads from each cDNA library were mapped onto the mouse genome build mm9 using tophat and the mappable data were then processed by Cufflinks (Trapnell et al.). The obtained data were normalized based on RPKM (reads per kilobase exon model per million mapped reads).
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: normalized rpkm files
 
Submission date Apr 11, 2013
Last update date May 15, 2019
Contact name Golnaz Vahedi
Organization name National Institutes of Health
Department NIAMS
Lab Lymphocyte Cell Biology Section
Street address 9000 Rockville Pike Bldg 10 Rm 13C101A
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL13112
Series (1)
GSE45975 Bach2 represses effector programmes to stabilize Treg-mediated immune homeostasis
Relations
SRA SRX264226
BioSample SAMN02044266

Supplementary file Size Download File type/resource
GSM1120731_F2_mRNA_Th1_177.rpkm.gz 761.5 Kb (ftp)(http) RPKM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap