|
| Status |
Public on Mar 16, 2020 |
| Title |
ChIPseq_INPUT_CTR |
| Sample type |
SRA |
| |
|
| Source name |
Human prostate cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DU145
tissue: Human prostate cancer cell line
chip antibody: NA
|
| Treatment protocol |
None
|
| Growth protocol |
DU145 cells were cultured in Dulbecco´s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (Gibco), 1x L-glutamine (Gibco) and 1x Pen/Strep (Gibco).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
(ChIP-seq) Chromatin preparation and ChIP experiments were performed with the ChIP-IT High Sensitivity Kit from Active Motif (#53040) according to the manufacturer’s instructions.
Libraries were prepared according to Illumina instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ChIP-seq experiment
|
| Data processing |
ChIP-seq analysis: Alignment: Sequence reads of the samples without spike-in were mapped to the human genome (hg19) using BOWTIE (PubMed ID 19261174) with the option -m 1. Sequence of the reads of hte samples with spike-in were mapped to a synthetic genome containing the human and the fruit fly chromosomes (hg19+dm3).
ChIP-seq analysis: Peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIP-seq genome-wide profiles without spike-in were normalized by the total number of reads of each sample. ChIP-seq genome-wide profiles with spike-in were normalized by the total number of fly reads of each sample.
processed data files format and content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq/RNA-seq)
processed data files format and content: Files .bed (BED, ChIP-seq signal enriched regions)
Genome_build: hg19
|
| |
|
| Submission date |
Aug 09, 2019 |
| Last update date |
Mar 16, 2020 |
| Contact name |
Enrique Blanco |
| E-mail(s) |
enrique.blanco@crg.eu
|
| Phone |
+34 93 316 01 00
|
| Organization name |
Center for Genomic Regulation (CRG)
|
| Department |
Gene Regulation, Stem Cells and Cancer
|
| Lab |
Epigenetic Events in Cancer (L. Di Croce's lab)
|
| Street address |
Dr. Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE135623 |
PHF19 mediated regulation of proliferation and invasiveness in prostate cancer |
|
| Relations |
| BioSample |
SAMN12542323 |
| SRA |
SRX6686393 |
