|
| Status |
Public on Jun 17, 2017 |
| Title |
JunB_ChIP_expt1 |
| Sample type |
SRA |
| |
|
| Source name |
WT Th17 cells
|
| Organism |
Mus musculus |
| Characteristics |
time point: 48 h
chip antibody: JunB (N-17; sc-46x)
strain: C57Bl/6
|
| Growth protocol |
Naïve CD4+ T cells were sort purified and cultured in Th17 cell polarizing conditions in vitro for 48 hours. Sorted cells were seeded into 12 well plates coated with anti-hamster IgG secondary antibody in IMDM supplemented with 10% FBS, penicillin (10U/ml), streptomycin (10μg/ml, glutamine (2mM), gentamicin (50μg/ml), and β-mercaptoethanol (55μM). For TCR stimulation, cultures were provided anti-CD3ε (0.25μg/ml) and anti-CD28 (1μg/ml). Cultures were also supplemented with anti-IL-4 (2μg/ml) and anti-IFNγ (2μg/ml), in addition to IL-6 (20ng/ml) and TGFβ1 (0.3ng/ml).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Th17 cells were crosslinked and the resulting sonicate was subjected to immunoprecipitation using 10μg of anti-JunB or anti-JunD. Following reverse-crosslinking, ChIP and input samples were processed to obtain purified DNA.
Libraries were constructed from ChIP and Input DNA using the Kapa Hyper Prep Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw sequence reads were aligned to the mm10 genome using Bowtie 2.2.5 with settings "-k 1"
JunB peaks were called using MACS2 (ver 2.1.0.20150731) with settings "-g mm -q 0.0005 -m 15 50 --bw=200"
JunD peaks were called using MACS2 (ver 2.1.0.20150731) with settings "-g mm -q 0.01 –m 5 50 --bw=200"
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 peak files
|
| |
|
| Submission date |
May 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Maria Ciofani |
| E-mail(s) |
maria.ciofani@duke.edu
|
| Organization name |
Duke University Medical Center
|
| Department |
Immunology
|
| Street address |
207 Research Drive, 128 Jones Building
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE98412 |
Role of JunB in Th17 cell effector stability [ChIP-seq] |
| GSE98414 |
Role of JunB in Th17 cell effector stability |
|
| Relations |
| BioSample |
SAMN06857856 |
| SRA |
SRX2773918 |
