|
| Status |
Public on Nov 06, 2011 |
| Title |
Tat ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Jurkat-Tat T cells
|
| Organism |
Homo sapiens |
| Characteristics |
expression: HIV Tat protein
chip antibody: Tat
cell line: Jurkat
chip antibody manufacturer: Abcam
chip antibody catalog #: ab43014
|
| Growth protocol |
Jurkat-Tat cells were maintained in RPMI supplemented with 10% fetal bovine serum, 1%penicillin and streptomycin and 800 microg/ml of G418
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Jurkat-Tat cells in exponential growth phase were fixed with 1% formaldehyde (v/v) for 10 min at 37°C. Fixation was stopped by addition of glycine to a final concentration of 140mM. Cell were lysed and chromatin was digested with the micrococcal nuclease from S. aureus (Roche) for 90 min at 4°C according to the manufacturerâs instructions, resuspended in lysis buffer and sonicated with Misonix ultrasonic liquid processor . 1% of the lysate was used as an input control. Lysates were immunoprecipitated with 5μg of anti-Tat antibodies (Abcam ab43014) using the standard ChIP protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
chromatin ChIPed against HIV tat
|
| Data processing |
Alignment: Sequence reads if 76 bp were obtained and mapped to the human hg19 genomes using the Bowtie 0.12.7. All reads mapping with two or fewer mismatches were retained. Reads with more than one locations matched in the genome was discarded. Sequence unable to align in the first alignment iteration was trimmed trimmed 25 bp away from 3' end of reads and re-aligned to the genome.
Each chromosome was divided into 100 bp windows. Reads are normalized by total read counts. Significant peaks were defined by comparing Tat ChIP read count versus input DNA read count using Poisson distribution to calculate p-value enrichment.
final bed file used 10^-4 threshold requiring neighoring window also with p-value less than 10^-4
|
| |
|
| Submission date |
Jul 18, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Siavash K Kurdistani |
| E-mail(s) |
Skurdistani@mednet.ucla.edu
|
| Phone |
310-794-5194
|
| Fax |
310 206-5272
|
| Organization name |
University of California Los Angeles
|
| Department |
Biological Chemistry
|
| Street address |
615 Charles E. Young Dr. South, 337
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE30738 |
Genome-wide binding map of the HIV Tat protein to the human genome (ChIP-Seq) |
| GSE30739 |
Genome-wide binding map of the HIV Tat protein to the human genome |
|
| Relations |
| SRA |
SRX084584 |
| BioSample |
SAMN00672589 |
