|
| Status |
Public on Sep 09, 2020 |
| Title |
PC3 control HDAC1 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
prostate
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: prostate cancer
passages: 20-30
chip antibody: Rabbit polyclonal anti-HDAC1 #ab7028
|
| Treatment protocol |
PC-3 control and GDC-resistant cells was treated with vehicle, 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 MNase digested, 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 4000 |
| |
|
| Description |
Sample 41
|
| Data processing |
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19/GRCh37) using BWA (v0.5.9) with defautl parameters. Reads from spike-in samples were mapped to the meta reference genome containing hg19 and dm6 chromosomes.
Peak calling was performed using MASC2 (v2.0.10)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Mar 24, 2020 |
| 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 |
GPL20301 |
| Series (2) |
| GSE137209 |
Bromodomain and HDAC inhibitors equivalently suppress PI3K/AKT inhibition resistance in cancers |
| GSE147455 |
An epigenetic vulnerability in PI3K/AKT inhibition resistant cancers is targetable by both bromodomain and HDAC inhibitors |
|
| Relations |
| BioSample |
SAMN14439608 |
| SRA |
SRX7981737 |
