|
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.
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|
|
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
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|
|
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 |