|
Status |
Public on Apr 05, 2024 |
Title |
sgZNF397-3 |
Sample type |
SRA |
|
|
Source name |
LnCaP/AR
|
Organism |
Homo sapiens |
Characteristics |
cell line: LnCaP/AR cell type: prostate cancer cell line genotype: sgZNF397 treatment: CSS
|
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 |
SAMN40188898 |
SRA |
SRX23780726 |