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Sample GSM1089819 Query DataSets for GSM1089819
Status Public on Oct 31, 2013
Title MDA231_MBD3
Sample type SRA
 
Source name MDA231_MBD3
Organism Homo sapiens
Characteristics cell line: MDA231
antibody: anti-MBD3 antibody (Abcam; ab91458)
Growth protocol Human breast cancer cell lines (MCF-7 and MDA-MB-231) were grown under standard conditions in DMEM/F12 supplemented with 10% fetal bovine serum and pen-strep.
Extracted molecule genomic DNA
Extraction protocol Cells were fixed with DSG (Disuccinimidyl glutarate) followed by formaldehyde. Chromatin was sonicated with Bioruptor to an average size of 0.3-0.6 kb. Chromatin was incubated with anti-MBD3 antibody (Abcam; ab91458) for 16hr followed by incubation with dynabeads A/G (Invitrogen). ChIP DNA was reverse-crosslinked and purified with Minelute PCR purification kit (Qiagen).
Library was prepared by TruSeq DNA Sample Prep kit (Illumina) or Nextera XT DNA sample prep kit (Illumina) according to the manufacturer's protocol.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
 
Description Library was prepared by TruSeq DNA Sample Prep kit or Nextera XT kit.
Data processing Basecalls performed using CASAVA version 1.7
Raw data from the replicates were merged.
Raw data was filtered by the following steps: reads were filtered if the average base quality score <20 and duplicate reads removed (based on identical sequences)
Reads were mapped against hg19 reference genome (excluding haplotype chromosomes) with Bowtie (v0.12.8 using the following parameters: -v 2 -m 1); HeK4 data were mapped against hg18 reference genome with ELAND program
Mapped data was filtered to remove hits with >2 mismatches to the reference genome.
Genome_build: hg19; hg18 for H3K4 data
Supplementary_files_format_and_content: bigwig file per sample per strand showing mapped read coverage; generated by BEDtools genomeCoverageBed and bedGraphToBigWig.
Supplementary_files_format_and_content: MBD3 bed files were generated by SICER v1.1 (redundancy threshold=1, window size=200, gap size=600, fragment size=300, FDR=0.001)
Supplementary_files_format_and_content: H3k4 wig files were generated by MACS-1.3.3 with default parameters.
 
Submission date Feb 28, 2013
Last update date May 15, 2019
Contact name Takashi Shimbo
E-mail(s) shimbot@niehs.nih.gov
Organization name NIH/NIEHS
Street address 111 TW Alexander Dr.
City RTP
ZIP/Postal code 27709
Country USA
 
Platform ID GPL15520
Series (1)
GSE44737 MBD3 localization by ChIP-seq
Relations
SRA SRX246862
BioSample SAMN01933037

Supplementary file Size Download File type/resource
GSM1089819_MDA231_MBD3.bw 289.8 Mb (ftp)(http) BW
GSM1089819_MDA231_MBD3_calledPeaks.bed.gz 304.0 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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