|
| Status |
Public on Aug 01, 2023 |
| Title |
16D_CRPC_DHT_AR_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
16D Prostate cancer cell line generated from mouse xenograft of LNCaP
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: ENZ-sensitive CRPC
treatment: None
disease state: AR positive, CRPC
|
| Treatment protocol |
16D cells were treated with DHT (10nM)before being used for ChIP seq sample preparation.
|
| Growth protocol |
16D cells were cultured in RPMI-1640 media containing 5% fetal bovine serum (Gibco #A3160701).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell lines were grown in media supplemented with 5% FBS (Gibco #A3160701) and processed for ChIP using either the Magna ChIP Kit (Millipore #17-10085) according to manufacturer’s instructions with the following antibody AR (5 µg, Cell Signaling #5153_CloneD6F11) or published protocol (PMID: 20680851) with the following antibody H3K27ac (10µg, ActiveMotif #39685).
For ChIP-seq, sequencing libraries (100 ng DNA per sample) were constructed using the KAPA library Prep Kit (Roche, Cat KK8510) with Illumina TruSeq indexes. Libraries were assessed for quality using gel electrophoresis and libraries passing quality control (e.g., no primer dimers) were quantified using the KAPA Library Quantification Kit for Illumina (Roche, Cat KK4824). Libraries were sequenced using the Illumina NextSeq 500 (75 bp single-end reads; cell lines).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
AZLab_Cseq4
|
| Data processing |
Basecalling was performed by Illumina Real Time Analysis (RTA) v2.11.3 with default settings
Demultiplexing was perfoemed by Illumina bcl2fastq v2.20.0.422 using parameters --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --barcode-mismatch 1
Raw reads were aligned to the hg38 (human) reference genome using BWA-MEM software (version 0.7.17) with default parameters. Alignments with mapping quality less than 60 were filtered out (leaving only uniquely mapped reads) and subsequently sam files were converted to bam files using Samtools software (version 1.1.2).
Narrow peaks were called using MACS2 callpeak (version 2.2.7.1) with options -f BAMPE -g 2.9e9 --keep-dup=1 -B -q 0.05. Broad peaks were called using MACS2 callpeak (version 2.2.7.1) with options -f BAM --broad -g 2.9e9 --keep-dup 1 --broad-cutoff 0.05. Bedtools intersect (v2.28.0) program suite was used to generate shared (-wa -u -f 0.5 -F 0.5 -e) and unique (-v -f 0.5 -F 0.5 -e) peak set between samples.
Custom bashscript was used to modify the utilization of Deeptools (v2.30.0) program suite to generate normalized bigwig files.
HOMER (v4.11) program suite was used to annotate peaks and perform motif enrichment analysis.
Assembly: hg38
|
| |
|
| Submission date |
Feb 02, 2023 |
| Last update date |
Aug 01, 2023 |
| Contact name |
Amina Zoubeidi |
| E-mail(s) |
azoubeidi@prostatecentre.com
|
| Organization name |
Vancouver Prostate Centre
|
| Street address |
2660 Oak Street
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6H 3Z6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE224421 |
ASCL1 is activated downsrteam of ROR2/CREB signaling pathway to support lineage plasticity [ChIP-seq] |
| GSE224422 |
ASCL1 is activated downsrteam of ROR2/CREB signaling pathway to support lineage plasticity. |
|
| Relations |
| BioSample |
SAMN33031317 |
| SRA |
SRX19267352 |
