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Sample GSM1322303 Query DataSets for GSM1322303
Status Public on May 23, 2014
Title Th9+Il1b_IN_VITRO_1hour
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: Naive T cells from spleen and nodes
Treatment protocol Differentiation was induced with 20 ng/ml IL-4 and 2 ng/ml TGFb with or without 10 ng/ml IL-1b in presence of IFNgamma blocking antibody for 1 hour or 3 days. For in vivo experiments, CD45.2 cells were injected 3 days after differentiation in CD45.1 mice and sorted 1 week later
Growth protocol CD4 T naive cells were isolated from C57/Bl6 WT 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 Th9 or Th9+Il-1b cells with Trireagent by following manufacturer protocol. Then, 1µg of total RNA was rRNA depleted thanks to Ribominus Eukaryote kit for RNAseq or polyA purified thanks to the NEBNext Poly(A) mRNA magentic isolation module
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 MiSeq
 
Description rRNA depleted RNA
Data processing Data were processed thanks to galaxy website
Fastq groomer tool was applied
Alignment was performed with TopHat on mm9 reference genome
Cufflink was applied
Genome_build: mm9
Supplementary_files_format_and_content: fpmk
 
Submission date Feb 05, 2014
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 GPL16417
Series (1)
GSE54697 Transcriptome analysis of Th9 CD4+ T cells differentiated with or without Il-1beta
Relations
BioSample SAMN02628474
SRA SRX465025

Supplementary file Size Download File type/resource
GSM1322303_Th9+Il1b_IN_VITRO_1hour.tabular.txt.gz 651.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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