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| Status |
Public on Jul 09, 2024 |
| Title |
LNCaP, Vehicle_CFS, 0, 24 hours, Rep3 |
| Sample type |
SRA |
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| Source name |
Prostate
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Prostate
cell line: LNCaP
cell type: epithelial
compound: Vehicle
dose: 0 nM
time: 24 hours
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| Treatment protocol |
LNCaP and VCaP cells were tretaed with vehicle, increasing concentrations of low-dose (0.01, 0.03, 0.06, 0.1 nM R1881) or High-Dose (10nM R1881) androgens for 24 hours
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| Growth protocol |
LNCaP cells (130,000 cells/well) were seeded in 6-well plates in RPMI 1640 supllemented with 8% charcoal dextran treated FBS(CFS). For VCaP cell line (300,000 cells/well), cells were seeded in 6-well plates in DMEM (8% CFS). 48 hrs later, cells were treated with R1881 for an additional 24 hrs
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The OMNI protocol was followed for ATAC-seq: https://doi.org/10.1038/nmeth.4396
ATAC-seq libraries were prepared using Nextera DNA Library Prep Kit.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
ATAC-seq reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.39.
Trimmed ATAC-seq reads were aligned to GRCh38/hg38 using BWA v0.7.17. Reads that were unaligned, multi-mapped, failed platform quality checks or had mapping quality less than 30 were removed.
Peaks were called and narrowPeak files were generated using MACS v2.2.7.1 with --pvalue 0.01, --keep-dup all, --call-summits, and -f BAMPE
BigWig files were generated using bamCoverage v3.5.1 from Deeptools suite, with --normalizeUsing RPGC, --binSize 10, --minFragmentLength 40, --effectiveGenomeSize 2701495761.
Assembly: GRCh38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak
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| Submission date |
Nov 13, 2023 |
| Last update date |
Jul 09, 2024 |
| Contact name |
Xiaodi Qin |
| Organization name |
Duke Cancer Institute
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| Street address |
2424 Erwin Road
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| City |
Durham |
| ZIP/Postal code |
27705 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE247591 |
Different doses of androgens induce the expression of distinct gene expression programs (ATAC-Seq) |
| GSE247593 |
Different doses of androgens induce the expression of distinct gene expression programs |
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| Relations |
| BioSample |
SAMN38237554 |
| SRA |
SRX22512997 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7893414_LNCaP_Vehicle-CFS-0_Rep3.sorted.fflt.odedup.bflt.bw |
306.2 Mb |
(ftp)(http) |
BW |
| GSM7893414_LNCaP_Vehicle-CFS-0_Rep3_TR_peaks.narrowPeak.gz |
2.9 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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