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Sample GSM4023642 Query DataSets for GSM4023642
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

Supplementary file Size Download File type/resource
GSM4023642_ChIPseq_INPUT_CTR.bedgraph.gz 85.2 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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