|
| Status |
Public on Apr 05, 2024 |
| Title |
sgNT_H3K4me3_2 |
| Sample type |
SRA |
| |
|
| Source name |
LnCaP/AR
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LnCaP/AR
cell type: prostate cancer cell line
chip antibody: Anti-Histone H3 (tri methyl K4) antibody - ChIP Grade (ab8580)
genotype: sgNT
|
| Treatment protocol |
For AR, H3K4me3 and H3K27ac ChIP, cells then were crosslinked with 1% PFA for 10 min and 0.125 M glycine for 5 min. For GFP-tagged ZNF397 ChIP, cells were two-step cross-linked with 2 mM DSG (Disuccinimidyl glutarate) for 45 min and 1% PFA for 10 min, cross-link were stopped by 0.125 M glycine for 5 min.
|
| 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 |
The DNA were sheared into 200-300 bp by Bioruptor® Pico, 1% sample was saved as input and the rest samples were incubated overnight with antibody for each reaction in 4 °C. Dynabeads Protein G was added to each reaction the next day and incubated for 4 hours in 4 °C. The samples were washed sequentially with low salt wash buffer, high salt wash buffer, LiCl wash buffer and TE buffer. DNA was eluted from the beads and reverse-crosslinked in 0.2M NaCl at 65°C for 4 hours. The input DNA and ChIPed DNA were prepared for ChIPseq.
ChIP-Seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep kit (NEB, E7103).
Illuminal NextSeq 2000 P2 100cycles
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
sgNT_H3K4me3.narrowpeak
|
| Data processing |
Raw sequencing reads were quality controlled using FastQC Tool (v0.11.9).
Reads were aligned to human reference genome assembly (GRCh38/hg38) using Bowtie 2 (v2.4.4, RRID: SCR_016368)90 with default parameters.
5hmC-Seq peaks were called using MACS2 (v2.1.2). Input DNA was used as the control for peak calling.
Assembly: hg38
Supplementary files format and content: FeatureCounts.csv (counts for called peaks); .narrowpeak file (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) |
| 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 |
SAMN40188868 |
| SRA |
SRX23780480 |
