|
| Status |
Public on Mar 07, 2018 |
| Title |
H3K4me1_siARV_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Prostate cancer 22Rv1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 22Rv1
cell type: prostate cancer cells
treatment: siARV
treatment: EtOH
chip antibody: H3K4me1(ab8895,abcam)
|
| Treatment protocol |
22Rv1 cells were transfected with non-target siRNA (designated as ARFL+/ARVs+), siRNA targeting ARV1/3/4/7 (designated as ARFL+/ARVs-) or siRNA targeting AR exon7 (designated as ARFL-/ARVs+), cultured with charcoal-stripped serum (CSS) medium for 72 hours, then treated with or without androgen (R1881) .
|
| Growth protocol |
Prostate cancer cells were cultures (typically 2–3 × 106 cells into a T75 flask) in RPMI 1640 medium (Gibco, Unite State) with charcoal-stripped (steroid depleted) serum (CSS).
|
| 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 Illumina HiSeq 2000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| 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 BWA (v0.5.9) with defautl parameters
Peak calling was performed using MASC2 (v2.0.10)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated from bedGraph files that generated from MACS, Scores represent reads coverage siganl
|
| |
|
| Submission date |
Nov 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhenqing Ye |
| E-mail(s) |
iamyezhenqing@gmail.com
|
| 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 |
GPL11154 |
| Series (2) |
| GSE80742 |
Identification and characterization of androgen receptor splice variants preferred bindings that drive prostate cancer progression [ChIP-seq] |
| GSE80743 |
Identification and characterization of androgen receptor splice variants preferred bindings that drive prostate cancer progression |
|
| Relations |
| BioSample |
SAMN06064328 |
| SRA |
SRX2379028 |
