|
| Status |
Public on Oct 02, 2017 |
| Title |
Th9 WT IP with IRF8 antibody |
| 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 |
Th9 differentiation was induced with IL-4 (20ng/ml) and TGF-β (2ng/ml) in presence of IFNγ blocking antibody for few hours, Th2 differentiation was induced with IL-4 (10ng/ml) in presence of IFNγ blocking antibody for few hours,
|
| 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 |
genomic DNA |
| Extraction protocol |
Crosslinking, extraction and shearing of chromatin was performed by using the Truchip chromatin shearing reagent kit from 300,000 cells by following manufacturer protocol. Then, sheared chromatin was immunoprecipitated with different antibodies by using the Active Motif's ChIP IT Kit by following manufacturer's instructions
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra DNA Library Prep Kit for Illumina. After library validation on a fragment analyzer, 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 |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Data were processed thanks to galaxy website
Fastq groomer tool was applied
Alignment was performed with Bowtie2 on mm10 reference genome
MACS was applied
MACS files were used on the NEBULLA website
Genome_build: mm10
Supplementary_files_format_and_content: BED
|
| |
|
| 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) |
| GSE99165 |
Chromatin interaction analysis of transcription factors and IRF8 in CD4+ T cells differentiated from wild-type mice |
| GSE99167 |
CD4+ T cells |
|
| Relations |
| BioSample |
SAMN07152066 |
| SRA |
SRX2840868 |
