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Sample GSM1340262 Query DataSets for GSM1340262
Status Public on Nov 26, 2014
Title human prostate tissue_H3K4me3 ChIP
Sample type SRA
Source name prostate tissue_H3K4me3 ChIP
Organism Homo sapiens
Characteristics tissue: human prostate tissue
factor: H3K4me3
cuture condition: untreated, cultured in RPMI+10%FBS
chip antibody: anti-H3K4me3
chip antibody vendor: Diagenode
chip antibody cat. #: pAb-003-050
Treatment protocol no treatement
Growth protocol RPMI & 10% Foetal Bovine Serum supplemented with G418 for the stable nucARRB1 lines
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Data processing Single-end 36 bp reads generated by the Illumina HiSeq 2000 were aligned against the Human Reference Genome (assemby GRCh37, NCBI Build 37) using BWA version 0.5.9. Reads were filtered by removing those with a BWA alignment quality score less than 15 as well as duplicate reads.
Enriched regions of the genome were identified by comparing ChIP samples to input samples using MACS Version 1.4.2
Genome_build: GRCh37
Supplementary_files_format_and_content: MACS peaks in .txt file
Submission date Mar 05, 2014
Last update date May 15, 2019
Contact name Chandra Chilamakuri
Organization name Cancer Research UK Cambridge Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
Platform ID GPL10999
Series (2)
GSE55615 Nuclear ARRB1 induces pseudohypoxia and cellular metabolism reprogramming in prostate cancer [ChIP-seq]
GSE55616 ARRB1 regulates prostate cancer cell metabolism
BioSample SAMN02673401
SRA SRX481465

Supplementary file Size Download File type/resource
GSM1340262_SLX-4353.707.s_6_peaks.txt.gz 509.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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