|
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 School of Medicine
|
Department |
Integrative Immunobiology
|
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 |