|
| Status |
Public on Jan 17, 2013 |
| Title |
input DNA |
| Sample type |
SRA |
| |
|
| Source name |
Jurkat_input
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Jurkat Trex (Invitrogen)
chip antibody: none
|
| Treatment protocol |
cells were induced with 1 ug/mL doxycycline for ~16 hours to allow for use as an appropriate comparison control with any other Jurkat Trex lines that carry a Tet-inducible construct.
|
| Growth protocol |
cells were maintained in RPMI-1640 media containing 10% FBS, penicillin, streptomycin, and 10 ug/mL Blasticidin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Approximately 1e8 cells in 100ml of media (approx 1e6 cells/ml) were treated with 1% formaldehyde for 15 minutes. Solubilized chromatin was prepared by incubation with lysis buffers, a few cycles of sonication and MNase treatment to obtain an average DNA size of ~1kb. ChIP was performed with anti-RUNX1 polyclonals.
Purified ChIP or input DNA was further sheared to an average size of ~200bp using a BioRuptor. The ends of the DNA fragments were polished using an Epicentre End-IT kit, polyadenylated with dATP and Klenow exo- and ligated to adapters, followed by 10 rounds of PCR with high fidelty Taq.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 2
|
| Data processing |
reads were mapped to hg19 using bowtie version 0.12.7
peaks were called for each replicate separately using the same input control with PeakRanger 1.15
Consensus peaks of each replicate were identified using the bedtools 2.17.0 utility intersectBed with a minimum overlap of 200. The start position of the consensus region is the minimum position of the two replicates and the end position is the maximum of the two replicates.
Consensus peaks were filtered such that both replicate peaks had a PeakRanger FDR value of 1e-7 or better.
FDR-filtered consensus peak regions were used to discover the top scoring motif with CUDA-MEME 2.7.3, and these peaks were filtered such that there was one instance of the motif TGYGGYY.
Genes were assigned to consensus peaks using GREAT version 2.0.2.
Genome_build: hg19
Supplementary_files_format_and_content: one bed file for each replicate that includes their PeakRanger FDR value; one tab file representing the consensus peaks and the identity of the replicates making them up
|
| |
|
| Submission date |
Nov 28, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Nevan Krogan |
| E-mail(s) |
nevan.krogan@ucsf.edu
|
| Phone |
415-476-2980
|
| Fax |
415-514-9736
|
| Organization name |
University of California, San Francisco
|
| Department |
Cellular & Molecular Pharmacology
|
| Lab |
Krogan
|
| Street address |
1700 4th Street
|
| City |
San Francisco |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE42575 |
CBFb Stabilizes HIV Vif to Counteract APOBEC3 at the Expense of RUNX1 Target Gene Expression [ChIP-seq] |
| GSE42576 |
CBFb Stabilizes HIV Vif to Counteract APOBEC3 at the Expense of RUNX1 Target Gene Expression |
|
| Relations |
| SRA |
SRX206836 |
| BioSample |
SAMN01820139 |
