|
| Status |
Public on Sep 28, 2015 |
| Title |
Resistant line BRD4 ChIP |
| Sample type |
SRA |
| |
|
| Source name |
Resistant line
|
| Organism |
Mus musculus |
| Characteristics |
tissue: haematopoietic progenitors
condition: Resistant
strain: C57BL/6
chip antibody: BRD4
|
| Treatment protocol |
Cell lines were grown in 0.1% DMSO or 600nM of I-BET151
|
| Growth protocol |
Cell lines were grown in RPMI-1640 supplemented with murine IL-3 (10 ng/mL), 20% fetal calf serum, penicillin (100 units/mL), streptomycin (100 ug/mL), amphotericin B (250ng/mL) and gentamycin (50 ug/mL)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysate were isolated from formaldehybe cross-linked cells and sonicated to release the chromatin, then immunoprecipitated with antibody
ThruPLEXTM-FD Prep Kit protocol (Rubicon Genomics)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8.2 software was used for basecalling.
Reads were aligned to the mm10 mouse genome using bwa 0.6.2-r126
Peak-calling was performed using MACS2
Normalised read counts for B-catenin ChIPs were generated with GenomicTools
Genome_build: mm10
Supplementary_files_format_and_content: bed files from MACS2 for BRD4 and H3K27ac ChIP
Supplementary_files_format_and_content: text file of normalised B-catenin ChIP read counts in 100bp bins around BRD4 peaks from sensitive line
|
| |
|
| Submission date |
Sep 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Mark Dawson |
| E-mail(s) |
mark.dawson@petermac.org
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Street address |
305 Grattan Street
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE63682 |
ChIP of BET proteins in iBET resistance [ChIP-seq] |
| GSE63683 |
iBET resistance |
|
| Relations |
| SRA |
SRX1293139 |
| BioSample |
SAMN04121942 |
