|
| Status |
Public on Jun 05, 2024 |
| Title |
ATAC_LN-tet-ARV7_CSS_DHT_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP-tet-ARV7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP-tet-ARV7
cell type: Prostate Cancer Cell Line (generated from LNCaP)
treatment: 10nM DHT in 5 percent CSS
|
| Treatment protocol |
LN-tet-ARV7 cells were grown in 5%CSS and treated with or without doxycycline for 2 days and stimulated with or without DHT.
|
| Growth protocol |
LN-tet-ARV7 cells are cultured routinely in 10% tetracycline-free FBS containing RPMI1640 and passed every 5-6 days
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Around 50,000 LN-tet-ARV7 cells treated with or without doxycycline or DHT were collected and lysed. Nuclei were collected and treated with transposase using Illumina Tagment DNA TDE1 Enzyme and Buffer Kit. DNA samples were then cleaned immediately with a Qiagen QIAquick Purification Kit and PCR preamplified by NEBNext High-Fidelity 2× PCR Master Mix. qPCR amplification was used to determine the additional cycles to prevent overamplification. The final PCR product was purified by Qiagen QIAquick Purification Kit.
ATAC-seq DNA Library were prepared with NEBNext ChIP-Seq Library Prep Reagent set for Illumina
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
ATAC_LN-tet-ARV7_CSS_DHT.narrowPeak
ATAC_LN-tet-ARV7_CSS_DHT.bw
|
| Data processing |
The sequence quality of raw reads was checked by FastQC (v.0.11.5).
The replicate of raw reads of each sample merged and mapped to the hg19 human genome using bwa (v0.7.5a) with aln and samse sub-commands.
Samtools (version 1.2) was used to convert sam files to bam format.
MACS3 (v3.0.0a6) was used to call peak on the bam files.
The bedGraph files from MACS were converted into bigwig files using UCSC tools (version 372)
Assembly: Human hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
|
| |
|
| Submission date |
Dec 16, 2022 |
| Last update date |
Jun 05, 2024 |
| Contact name |
Maryam Labaf |
| E-mail(s) |
maryam.labaf001@umb.edu
|
| Organization name |
University of Massachusetts Boston
|
| Department |
Biology
|
| Lab |
Cai Lab
|
| Street address |
100 William T Morrissey Blvd
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02125 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE221137 |
ATAC-seq analyses of AR-V7. |
| GSE221142 |
Distinct activity of androgen receptor splice variants in promoting prostate cancer metastasis |
|
| Relations |
| BioSample |
SAMN32271809 |
| SRA |
SRX18725487 |
