|
| Status |
Public on Apr 05, 2024 |
| Title |
sgNT_5hmC_ChIPed_1 |
| Sample type |
SRA |
| |
|
| Source name |
LnCaP/AR
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LnCaP/AR
cell type: prostate cancer cell line
fraction: IP
genotype: sgNT
|
| Treatment protocol |
NA
|
| 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 |
Genomic DNA were extracted and sheared into fragments with an average size of 200 bp. 60 μg sonicated genomic DNA used in glucose transfer reaction and then proceeded biotinylation reaction. DNA were captured by Dynabeads Myone Streptavidin C1 (Invitrogen™ 65001) and libraries were prepared.
Libraries were prepared by using NEBNext1100 ® Ultra™ II DNA Library Prep kit (NEB, E7103)
Illuminal NextSeq 2000 P2 100cycles
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| 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.
Counts for called peaks were done using FeatureCounts (v1.5.3) .
Assembly: hg38
Supplementary files format and content: csv (counts for called peaks)
Library strategy: 5hmC
|
| |
|
| 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 |
| GSE260466 |
Overcoming Lineage Plasticity and AR-Targeted Therapy Resistance in ZNF397-Deficient Prostate Cancer via TET2 Inhibition [5hmC-seq] |
|
| Relations |
| BioSample |
SAMN40188863 |
| SRA |
SRX23780461 |
