|
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 |