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Sample GSM2634710 Query DataSets for GSM2634710
Status Public on Oct 02, 2017
Title Th1 WT day 2 B
Sample type SRA
 
Source name Naive T cells from spleen and nodes
Organism Mus musculus
Characteristics strain: C57/Bl6j
age: 7 weeks
genotype: Wild-type
cell type: CD4 T cells
Treatment protocol Th1 differentiation was induced with IL-12 (10ng/ml) in presence of IL-4 blocking antibody for 1 or 2 days. Th2 differentiation was induced with IL-4 (10ng/ml) in presence of IFNγ blocking antibody for 1 or 2 days. Th9 differentiation was induced with IL-4 (20ng/ml) and TGF-β (2ng/ml) in presence of IFNγ blocking antibody for 1 or 2 days. Th17 differentiation was induced with IL-6 (20ng/ml) and TGF-β (2ng/ml) in presence of IFNγ and IL-4 blocking antibodies for 1 or 2 days. Treg differentiation was induced with TGF-β (4ng/ml) in presence of IFNγ and IL-4 blocking antibodies for 1 or 2 days.
Growth protocol CD4 T naive cells were isolated from C57/Bl6 Wt and CD4cre IRF8flox mice. Differentiation was induced in RPMI culture medium complemented with 10% FBS,1% antibiotics in CD3/CD28 coating plates
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from 300,000 CD4+ T cells with Trireagent by following manufacturer protocol. Then, 1µg of total RNA was rRNA depleted thanks to Ribominus Eukaryote kit for RNAseq or mRNA purified thanks to NEB kit
Libraries were prepared according to Bioo Scientific's instructions accompanying the Nextflex RNA Seq-Kit for Illumina. Briefly, RNA was heat fragmented and double strand cDNA synthesis was performed in 2 steps. After purification, the double strand cDNA was end repaired and then adenylated. After adapter ligation, DNA was PCR amplified for 12 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were obtained. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq device following the manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description rRNA depleted RNA
Data processing Data were processed thanks to galaxy website
Fastq groomer tool was applied
Alignment was performed with TopHat on mm10 reference genome
Cufflink was applied
Genome_build: mm10
Supplementary_files_format_and_content: Tabular
 
Submission date May 22, 2017
Last update date May 15, 2019
Contact name Romain Boidot
E-mail(s) rboidot@cgfl.fr
Organization name CGFL
Lab Molecular Biology Unit
Street address 1, rue Pr Marion
City Dijon
ZIP/Postal code 21079
Country France
 
Platform ID GPL19057
Series (2)
GSE99166 Transcriptome analysis of CD4+ T cells differentiated from wild-type and CD4cre IRF8flox mice
GSE99167 CD4+ T cells
Relations
BioSample SAMN07152089
SRA SRX2840889

Supplementary file Size Download File type/resource
GSM2634710_Th1_WT_day2_B.fpkm_tracking.gz 757.8 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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