|
| Status |
Public on Mar 11, 2021 |
| Title |
CTCF_45_Hilar_LN |
| Sample type |
SRA |
| |
|
| Source name |
CTCF ChIP Sample 45 Hilar lymph node
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: metastatic castration resistant prostate cancer
tissue: Hilar lymph node
chip-antibody: Millipore, 07-729, lot#2887267
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Illumina Hi-seq 2500, 65bp single-end reads
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Chromatin IP for CTCF in Sample 45_Hilar_LN
|
| Data processing |
Raw sequencing data were aligned using BWA v0.5.20 to hg19 and filtered for mapping quality > MQ20 with samtools version 1.8
Duplicate reads were marked with Picard MarkDupes function (version 2.18)
Peaks were called for each sample against it's own input DNA using two peakcallers, MACS2 (v2.1.1) and DFilter (v1.5).For MACS2, we called peaks with the callpeaks function with no model, using a q value threshold cutoff of 0.01 and the fragment size input of the individual sample as determined using phantompeaks (v1.14). Peaks were also called with DFilter using default parameters. We then took the intersect of the peaks called from both peak callers using bedTools intersect (v2.26.0).
Genome_build: hg19
Supplementary_files_format_and_content: peak files in bed format with macs2 output
|
| |
|
| Submission date |
Jun 02, 2020 |
| Last update date |
Mar 12, 2021 |
| Contact name |
Tesa Severson |
| E-mail(s) |
t.severson@nki.nl
|
| Organization name |
Netherlands Cancer Institute
|
| Department |
Molecular Carcinogensis
|
| Street address |
121 Plesmanlaan
|
| City |
Amsterdam |
| ZIP/Postal code |
1066 CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE151619 |
Epigenetic and transcriptional analysis reveals a core transcriptional program conserved in clonal prostate cancer metastases [ChIP-seq] |
| GSE152231 |
Epigenetic and transcriptional analysis reveals a core transcriptional program conserved in clonal prostate cancer metastases |
|
| Relations |
| BioSample |
SAMN15081178 |
| SRA |
SRX8453145 |
