|
| Status |
Public on Nov 07, 2023 |
| Title |
22Rv1_GR_siNON_Dex_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
22Rv1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CWR22 xenograft derived human prostate carcinoma epithelial cell line
cell line: 22Rv1
enz treatment: 0
sirna treatment: Non-targeting control siRNA (Dharmacon, D-001810-10)
hormone treatment: dexamethasone
hormone concentration: 100 nM
chip antibody: GR (Cell Signaling, 12041)
|
| Treatment protocol |
22Rv1 cells were grown in the presence or absence of 10 µM enzalutamide (ENZ) for at least 21 days (ENZ3w) before the start of hormone treatments. For siRNA treatments, the 22Rv1 cells were transfected with 80 nM siRNA using Lipofectamine RNAiMAX reagent 96 h before hormone treatments. 22Rv1 cells were treated with vehicle (EtOH) or 100 nM of Dexamethasone (Dex) for 1 h before the start of ChIPs.
|
| Growth protocol |
22Rv1 cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin, 1 µg/ml streptomycin and 2 mM L-glutamine. All cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, after 1% formaldehyde crosslinking, cells were harvested, chromatin was sonicated to 100-300 bp fragments, and protein-DNA complexes were isolated with specified antibody.
ChIP-seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit according to instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
100SE
|
| Data processing |
Basecalls performed using CASAVA, and FASTX-toolkit was used to trim low quality reads.
The reads were aligned to human reference genome version hg38 by using Bowtie2 software version 2.3.4.1. with end-to-end sensitive mode allowing no mismatches.
Peaks were called using HOMER program version 4.10. using findPeaks with style factor, FDR<0.01, >25 tags, >4-fold over control sample and local background. Corresponding EtOH sample was used as the control sample.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.
|
| |
|
| Submission date |
Sep 20, 2023 |
| Last update date |
Nov 07, 2023 |
| Contact name |
Ville Paakinaho |
| E-mail(s) |
villepaakinaho@gmail.com
|
| Organization name |
University of Eastern Finland
|
| Department |
School of Medicine
|
| Lab |
Biomedicine
|
| Street address |
Yliopistonranta 8
|
| City |
Kuopio |
| ZIP/Postal code |
70210 |
| Country |
Finland |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE214754 |
Chromatin accessibility and pioneer factor FOXA1 restrict glucocorticoid receptor action in prostate cancer (ChIP-Seq) |
| GSE214757 |
Chromatin accessibility and pioneer factor FOXA1 restrict glucocorticoid receptor action in prostate cancer |
|
| Relations |
| BioSample |
SAMN37482475 |
| SRA |
SRX21840301 |
