|
| Status |
Public on Apr 05, 2024 |
| Title |
Ctrl, Input |
| Sample type |
SRA |
| |
|
| Source name |
LnCaP/AR
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LnCaP/AR
cell type: prostate cancer cell line
chip antibody: none
treatment: 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 dihydrotestosterone (DHT) for 4 hours.
|
| Growth protocol |
LNCaP/AR cells were cultured 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 |
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico sonication device.
ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep kit (NEB, Cat E7103). 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit by Agilent 2100 Bioanalyzer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw sequencing reads from ChIP-Seq experiments were quality controlled using FastQC Tool (v0.11.9) and aligned to human reference genome assembly (GRCh38/hg38) using Bowtie2 (v2.4.4) with default parameters.
Duplicated reads were removed using Picard MarkDuplicates (v2.26.11).
ChIP-Seq peaks were called using MACS2 (v2.1.2).
Genome browser tracks were generated using bamCoverage (v2.4.1) with parameter “—normalizeUsingRPKM” and visualized using Integrative Genomics Viewer.
Motif analysis was performed using homer (v4.11).
Assembly: hg38
Supplementary files format and content: bw, txt(peak files)
|
| |
|
| Submission date |
Apr 25, 2023 |
| 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 |
GPL18573 |
| Series (2) |
| GSE230600 |
Overcoming Lineage Plasticity and AR-Targeted Therapy Resistance in ZNF397-Deficient Prostate Cancer via TET2 Inhibition [ChIP-seq] |
| GSE230602 |
Overcoming Lineage Plasticity and AR-Targeted Therapy Resistance in ZNF397-Deficient Prostate Cancer via TET2 Inhibition |
|
| Relations |
| BioSample |
SAMN34371802 |
| SRA |
SRX20098610 |
