|
| Status |
Public on Sep 01, 2017 |
| Title |
H3K27me3 ChIPSeq_abl_EPZ treated |
| Sample type |
SRA |
| |
|
| Source name |
abl_EPZ treated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP-abl (abl)
cell types: castration resitant prostate cancer cells
cell phenotype: AR-positive, EZH2 inhibitor-sensitive
passages: 61-64
treated with: EPZ-6438
chip antibody: H3K27 trimethylation (Cell Signaling, C36B11, #9733S) and H2Av (Active Motif 39715)
|
| Treatment protocol |
Both types of cells were treated with vehicle (DMSO), GSK126 or EPZ-6438 at final concentrations of 5 uM for 4-5 days before the cells were crosslinked and collected.
|
| Growth protocol |
Both DU145 and LNCaP-abl (abl) cells were routinely maintained in phenol-red-free RPMI1640 with 10% charcoal-stripped FBS plus 1% Penicillin-Streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Prostate cancer cells were crosslinked with 1% formaldehyde and lysed in RIPA buffer with 0.3 M NaCl. ChIP DNA was purified using PCR Purification Kit (Qiagen) and then quantified by Quant-iTTM dsDNA HS Assay Kit (Invitrogen).
ChIP-Seq libraries were prepared using ThruPLEX-FD Prep Kit (Rubicon Genomics) according to the manufacturer's protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
abl_H3K27me3_EPZ
|
| Data processing |
FASTQ files were mapped to hg19 (Homo Sapiens) and dm3 (Drosophila melanogaster) assemblies respectively using BOWTIE (version 0.12.7); duplicated reads were removed.
ChIP-Seq peaks and bigwig files were called and generated using MACS2 (version 2.1.0)
Genome_build: hg19 (human) and dm3 (drosophila)
Supplementary_files_format_and_content: BED files, containging the location of the peaks
Supplementary_files_format_and_content: BigWig files, containing the enrichment information
|
| |
|
| Submission date |
Apr 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kexin Xu |
| E-mail(s) |
kxuthscsa@gmail.com
|
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Molecular Medicine
|
| Street address |
7703 Floyd Curl, MC 8257
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE80238 |
Gemone-wide changes of epigenetic mark H3K27 trimethylation (H3K27me3) and AR in prostate cancer cells upon the treatment of EZH2 inhibitors [ChIP-seq] |
| GSE80240 |
Distinct changes in transcriptional profiles and epigenetic patterns mediated by EZH2 inhibitors in sensitive and insensitive prostate cancer cells |
|
| Relations |
| BioSample |
SAMN04849721 |
| SRA |
SRX1702473 |
