|
| Status |
Public on Sep 09, 2020 |
| Title |
GDC-R_SAHA_BRD4_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
prostate
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: prostate cancer
passages: 20-30
cell line: PC-3
chip antibody: Rabbit monoclonal anti-BRD4 Abcam ab128874
|
| Treatment protocol |
PC-3-control and PC-3-GDC-R cells were treated with DMSO, or iCBP112, or SAHA for 24 hours
|
| Growth protocol |
Cells were maintained at 37°C and 5% CO2 in RPMI 1640 containing 10% fetal bovine serum (FBS) and 1% antibiotic/antimycotic (Thermo Fisher Scientific).FGF-2 (NS expansion medium).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using bowtie2 with defautl parameters
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated by bedGraphToBigWig, and peaks were called by Macs2
|
| |
|
| Submission date |
Sep 10, 2019 |
| Last update date |
Sep 09, 2020 |
| Contact name |
Zhenqing Ye |
| E-mail(s) |
[email protected]
|
| Organization name |
UT Health San Antonio
|
| Department |
6Department of Population Health Sciences
|
| Street address |
8403 Floyd Curl Dr
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE137207 |
Pattern occupation of HDACs on chromatin determines PI3K/AKT inhibitor resistance in cancers [ChIP-seq] |
| GSE137209 |
Bromodomain and HDAC inhibitors equivalently suppress PI3K/AKT inhibition resistance in cancers |
|
| Relations |
| BioSample |
SAMN12723263 |
| SRA |
SRX6827763 |
