|
| Status |
Public on May 23, 2014 |
| Title |
Th9_IN_VITRO_Day_3 |
| 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 |
PolyA purified mRNA
|
| 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 |
SAMN02628475 |
| SRA |
SRX465026 |
