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Sample GSM1330733 Query DataSets for GSM1330733
Status Public on May 27, 2015
Title BJ_H3K4me1
Sample type SRA
 
Source name BJ (hTert/sT)
Organism Homo sapiens
Characteristics tissue: skin
cell type: fibroblast cell line
chip antbody: H3K4me1 (ab8895, Abcam)
cell line: BJ
treatment: none
tiime: untreated
Treatment protocol Fibroblast cells were treated with H2O2 (final concentration 0.2mM) for 30 minutes and 2 hours.
Growth protocol Fibroblast cells were routinely generated typically by re-plating 1-2 10e6 cells into a 140x20mm plate on uncoated plastic in DMEM medium (Gibco, Life technologies) supplemented with BSF and penicillin/streptomycin.
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 HiSeq 2000
 
Data processing Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the following configurations : -v 2 -m 1 -p 2 --best --strata --quiet --solexa1.3-quals
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, wig files were generated from the BAM alignment files using BedTools genomeCoverageBed (v2.14.2); bedGraph files were automatically generated as an output of MACS 2.0.10
 
Submission date Feb 19, 2014
Last update date May 15, 2019
Contact name Jingxian Zhang
E-mail(s) zhangjingxian.nus@gmail.com
Organization name Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore
Department IMCB
Street address 61 Biopolis Drive Proteos
City Singapore
State/province Singpaore
ZIP/Postal code 138673
Country Singapore
 
Platform ID GPL11154
Series (2)
GSE55171 Pervasive genomic transcription during oxidative stress generates thousands of previously uncharacterized lncRNAs (ChIP-Seq)
GSE55172 Pervasive genomic transcription during oxidative stress generates thousands of previously uncharacterized lncRNAs
Relations
BioSample SAMN02645875
SRA SRX472906

Supplementary file Size Download File type/resource
GSM1330733_BJ_H3K4me1_treat_pileup.bedgraph.gz 8.5 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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