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Status |
Public on Apr 05, 2024 |
Title |
sgZNF397_H3K27ac_1 |
Sample type |
SRA |
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|
Source name |
LnCaP/AR
|
Organism |
Homo sapiens |
Characteristics |
cell line: LnCaP/AR cell type: prostate cancer cell line chip antibody: Anti-Histone H3 (acetyl K27) antibody - ChIP Grade (ab4729) genotype: sgZNF397
|
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.
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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
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
NextSeq 2000 |
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|
Description |
sgZNF397_H3K27ac.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)
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|
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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 |
SAMN40188873 |
SRA |
SRX23780475 |