|
| Status |
Public on Nov 07, 2023 |
| Title |
VCaP_ATAC_ENZ3w_naked-DNA_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
VCaP
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Vertebral Cancer of the Prostate
cell line: VCaP
enz treatment: 3 weeks
hormone treatment: EtOH vehicle
hormone concentration: 0.01%
|
| Treatment protocol |
VCaP and 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. VCaP and 22Rv1 cells were treated with vehicle (EtOH), 1 nM of dihydrotestosterone (DHT), or 100 nM of Dexamethasone (Dex) for 1 h before the start of nuclei extraction.
|
| Growth protocol |
VCaP cells were grown in DMEM medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin and 1 µg/ml streptomycin. 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 ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Tn5 Transposase loaded with sequencing adapters.
ATAC-seq libraries were prepared with loaded Diagenode Tagmentase (#C01070012) according to instructions.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
40PE
|
| 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 transposase treated naked DNA sample was used as the control sample.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.
|
| |
|
| Submission date |
Oct 04, 2022 |
| 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 |
GPL18573 |
| Series (2) |
| GSE214753 |
Chromatin accessibility and pioneer factor FOXA1 restrict glucocorticoid receptor action in prostate cancer (ATAC-Seq) |
| GSE214757 |
Chromatin accessibility and pioneer factor FOXA1 restrict glucocorticoid receptor action in prostate cancer |
|
| Relations |
| BioSample |
SAMN31149902 |
| SRA |
SRX17794320 |
