|
| Status |
Public on Apr 22, 2024 |
| Title |
PC3 cells, siNC, ChIP-JUN |
| Sample type |
SRA |
| |
|
| Source name |
PC3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PC3
cell type: Prostate cancer cell line
chip antibody: anti-JUN
treatment: Negative control knockdown
|
| Treatment protocol |
PC3,NCI-H660 cells were treated with vehicle versus ORY-1001, or C12 for 4hrs
|
| Growth protocol |
PC3,LNCaP cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. NCI-H660 cells were cultured in RPMI-1640 base medium supplemented with 5% FBS, 10nM β-estradiol, 10nM hydrocortisone, and 1% Insulin-Transferrin-Selenium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% formaldehyde and then sonicated. DNA were immunoprecipitatted with antibody and protein A/G beads. After reverse crosslinking, DNA were purifed with Qiagen PCR purification kit.
Libraries were constructed using the SMARTer ThruPLEX DNA-Seq Prep Kit (Takara Bio USA).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
PC3, JUN, CST
|
| Data processing |
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were mapped to the hg19 human genome using bwa (version 0.7.17-r1188) with aln and samse or sampe sub-commands.
Samtools (version 1.9) was used to convert sam files to bam format.
MACS2 (version 2.1.4) was used to call peak on the bam files.
bedGraph files generated from MACS2 were converted into bigwig files with UCSC tools (version 357).
Assembly: hg19
Supplementary files format and content: bigWig, bed
|
| |
|
| Submission date |
May 15, 2023 |
| Last update date |
Apr 22, 2024 |
| Contact name |
Zifeng Wang |
| E-mail(s) |
wzifeng8@gmail.com
|
| Phone |
6174709887
|
| Organization name |
UMASS Boston
|
| Department |
CPCT
|
| Lab |
Changmeng Cai
|
| Street address |
100 Morrissey Blvd, ISC/4610
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02125 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE232552 |
FOXA2/AP-1 drives prostate cancer lineage plasticity [ChIP-seq] |
| GSE232555 |
FOXA2/AP-1 drives prostate cancer lineage plasticity |
|
| Relations |
| BioSample |
SAMN35099526 |
| SRA |
SRX20355964 |
