|
| Status |
Public on Jun 05, 2024 |
| Title |
ChIP-FOXA1_LN-tet-ARV7_CSS_Veh_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP-tet-ARV7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP-tet-ARV7
cell type: Prostate Cancer Cell Line (generated from LNCaP)
antibody: FOXA1
treatment: vehicle in 5 percent CSS
|
| Treatment protocol |
LN-tet-ARV7, LN-tet-ARFL and LN-tet-ARV7-S81A cells were grown in 5%CSS (hormone-depelted) and treated with doxycycline for 2 days for ChIP V5, FOXA1 and H3K27ac, and stimulated with DHT for 4 hours for AR-C ChIP.
|
| Growth protocol |
LN-tet-ARV7, LN-tet-ARFL and LN-tet-ARV7-S81A cells are cultured routinely in 10% tetracycline-free FBS containing RPMI1640 and passed every 5-6 days
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with formaldehyde and then sonicated. DNA were immunoprecipitatted with V5, FOXA1, H3K27ac or AR-C antibody and protein A beads. After reverse crosslinking, DNA were purifed with Qiagen PCR purification kit.
ChIP DNA Library were prepared with NEBNext ChIP-Seq Library Prep Reagent set for Illumina and NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
ChIP-FOXA1_LN-tet-ARV7_CSS_Veh.narrowPeak
ChIP-FOXA1_LN-tet-ARV7_CSS_Veh.bw
|
| Data processing |
The sequence quality of raw reads was checked by FastQC (v.0.11.5).
The replicate of raw reads of each sample merged and mapped to the hg19 human genome using bwa (v0.7.5a) with aln and samse sub-commands.
Samtools (version 1.2) was used to convert sam files to bam format.
MACS3 (v3.0.0a6) was used to call peak on the bam files.
The bedGraph files from MACS were converted into bigwig files using UCSC tools (version 372)
Assembly: Human hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
|
| |
|
| Submission date |
Dec 16, 2022 |
| Last update date |
Jun 05, 2024 |
| Contact name |
Maryam Labaf |
| E-mail(s) |
maryam.labaf001@umb.edu
|
| Organization name |
University of Massachusetts Boston
|
| Department |
Biology
|
| Lab |
Cai Lab
|
| Street address |
100 William T Morrissey Blvd
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02125 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE221140 |
Cistrome analyses of AR-V7. |
| GSE221142 |
Distinct activity of androgen receptor splice variants in promoting prostate cancer metastasis |
|
| Relations |
| BioSample |
SAMN32271823 |
| SRA |
SRX18725439 |
