|
| Status |
Public on Apr 15, 2021 |
| Title |
HA ChIP-seq in shFoxA1+K295A LNCaP cells |
| Sample type |
SRA |
| |
|
| Source name |
prostate tumor
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
shRNA: stable expression of both shFoxA1 and K295A
antibody: HA
antibody vendor: Abcam
antibody catalog number: ab9110
antibodylot/batch number: GR3264065-1
|
| Treatment protocol |
For m880-m883, LNCaP cells were infected with shCtrl or shFOXA1 along with control, HA-FOXA1, or HA-K295A for 5 days. For m944-m951, LNCaP cells were treated with either DMSO, 1 uM EPZ-6438, 3 uM P5091, or in combination for 7 days.
|
| Growth protocol |
LNCaP cells were maintained in RPMI supplemented with 10% FBS and 1% penicillin and streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin in nuclear fraction were sheared to 200-500bp using an Covaris M220 Focused-ultrasonicator, Lysates were clarified from sonicated nuclei and protein-DNA complexes were immunoprecipitated using the indicated antibody. DNA was then reverse crosslinked from protein and purified. ChIP-seq libraries were prepared from 3-5ng ChIPped DNA by using NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer’s instructions. Postamplification libraries were size selected at 250–450 bp in length using Agencourt AMPure XP beads from Beckman Coulter and were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4603). Libraries were pooled to a final concentration of 10nM and sequenced single-end using the Illumina HiSeq 4000.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
LNCaP cells with stable expression of both shFoxA1 and K295A
|
| Data processing |
Reads were aligned to the hg19 reference human genome using bowtie2
Peak-calling by HOMER v4.2
Genome_build: hg19
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file and peak txt file
|
| |
|
| Submission date |
Nov 16, 2020 |
| Last update date |
Apr 15, 2021 |
| Contact name |
Jindan Yu |
| E-mail(s) |
jindan.yu@emory.edu
|
| Organization name |
Emory University
|
| Department |
Urology
|
| Lab |
Jindan Yu's lab
|
| Street address |
E330, 1760 Haygood Dr NE
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL15456 |
| Series (2) |
| GSE161517 |
Regulation of FOXA1 protein stability by Polycomb and BUB3/USP7 deubiquitin complexes in prostate cancer [ChIP-Seq] |
| GSE161519 |
Regulation of FOXA1 protein stability by Polycomb and BUB3/USP7 deubiquitin complexes in prostate cancer |
|
| Relations |
| BioSample |
SAMN16809030 |
| SRA |
SRX9513899 |
