|
| Status |
Public on Apr 05, 2024 |
| Title |
sgNTDHT-3 |
| Sample type |
SRA |
| |
|
| Source name |
LnCaP/AR
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LnCaP/AR
cell type: prostate cancer cell line
genotype: sgNTDHT
treatment: CSS 10nM DHT
|
| Treatment protocol |
LNCaP/AR cells were starved in RPMI medium supplemented with 10% charcoal-stripped serum (CSS), 1% L-glutamine, 1% penicillin-streptomycin, 1% HEPES, and 1% sodium pyruvate for 3 days and treated with Vehicle (0.1% Ethanol) or dihydrotestosterone (DHT) for 4 hours.
|
| Growth protocol |
LNCaP/AR cells were maintained in RPMI medium supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, 1% penicillin-streptomycin, 1% HEPES, and 1% sodium pyruvate. Cells were split 1 to 6 every 3 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
80,000 LnCaP/AR cells were used in ATACseq assay, the libraries were prepared by Active Motif ATAC-seq kit (#53150).
Follow the instructions of Active Motif ATAC-seq kit (#53150).
Illuminal NextSeq 2000 P2 100cycles
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Data were analyzed as the following: FastQC Tool (v0.11.8) was used for quality control and pre-processing (https://github.com/s-andrews/FastQC).
Alignment to human genome GRCh38 was performed using Bowtie 2 (v2.4.2).
Accessible chromatin peaks were called using MACS3 (v3.0.0, https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-9-r137) with ‘BAMPE’ mode and q-value cutoff at 0.01.
Assembly: hg38
Supplementary files format and content: narrowPeak (information on called peaks)
|
| |
|
| Submission date |
Feb 28, 2024 |
| Last update date |
Apr 05, 2024 |
| Contact name |
Ping Mu |
| E-mail(s) |
muping817@gmail.com
|
| Organization name |
University of Texas Southwestern Medical Cente
|
| Street address |
5323 Harry Hines Blvd.
|
| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE230602 |
Overcoming Lineage Plasticity and AR-Targeted Therapy Resistance in ZNF397-Deficient Prostate Cancer via TET2 Inhibition |
| GSE260467 |
Overcoming Lineage Plasticity and AR-Targeted Therapy Resistance in ZNF397-Deficient Prostate Cancer via TET2 Inhibition [ATAC-seq] |
|
| Relations |
| BioSample |
SAMN40188901 |
| SRA |
SRX23780723 |
