|
| Status |
Public on Oct 25, 2017 |
| Title |
KO 1 |
| Sample type |
SRA |
| |
|
| Source name |
Activated CD4+ T cell under IL6+TGFbR inhibitor condition
|
| Organism |
Mus musculus |
| Characteristics |
background: C57BL/6
gender: pooled male and female
tissue: Spleen+Lymph nodes
cell type: CD4+T cell
timepoint: 12 hour post treatment
treatment: IL6+TGFbR inhibitor
genotype: CD4cre;Smad4fl/fl
antibody: Smad4
|
| Treatment protocol |
CD4+ T cells were activated and cultured under IL6+TGFbR inhibitor condition
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested and fixed with FA for 20min at 37C. And then performed ChIP.
Libraries were constructed with the use of the Illumina TruSeq DNA library construction kit V2 according to manufacturer's protocol. Libaries were pooled and sequenced on the Illumina NextSeq500 sequencer
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw reads were first cleaned for adapter sequences using Trim Galore with default parameters;
ChIP-Seq reads (~60M per sample) were aligned to the UCSC mm10 reference genome using Bowtie1. Duplicate reads are removed.
FindPeaks from Homer (Version 4.8.3) was used to call all reported ChIP-seq peaks with default parameters and “-F 2 -L 0 -C 1.5 -fdr 0.005"; Peak calling for all samples used pooled input sample as noise control.
Genome_build: mm10
Supplementary_files_format_and_content: bed
|
| |
|
| Submission date |
Jul 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yisong Wan |
| Organization name |
University of North Carolina-Chapel Hill
|
| Department |
Lineberger Comprehensive Cancer Center
|
| Lab |
Marsico Hall Rm 5229J
|
| Street address |
125 Mason Farm Road
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE101593 |
Reversing SKI–SMAD4-mediated suppression is essential for TH17 cell differentiation [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN07363064 |
| SRA |
SRX3014619 |
