Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MBD2

Cell type

Cell type Class
Breast
Cell type
HMLE
NA
NA

Attributes by original data submitter

Sample

source_name
cell line
cell line
HMLER
protocol
sonication, MBD2 ChIP
chip antibody
a custom-made rabbit polyclonal serum obtained after immunization with peptides corresponding to the N-terminal part of the MBD2 protein (Covalab, Villeurbanne, Lyon) (Perriaud et al. Curr. Pharm. Des 2013)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Genomic DNA was sheared to a mean fragment length of 300-500 bp through sonication. Methylated-DNA precipitation (MeDP) was carried out using the MethylMiner Methylated DNA Enrichment Kit (Life Technologies) from 1µg of sheared DNA. Pools of 5 independent experiments, library preparation and high throughput sequencing (single-end 50 bp sequencing on Illumina HiSeq 2000) were performed at Beijing Genomics Institute (Hong-Kong, China). MBD2 Chromatin Immunoprecipitations (ChIP) were performed as previously described (Auriol et al. Nucleic Acids Research 2005). Briefly, sheared chromatin (with a mean fragment length between 300 and 500 bp) was obtained by sonication of formaldehyde cross-linked nuclei. ChIP was then performed with a custom-made rabbit polyclonal serum obtained after immunization with peptides corresponding to the N-terminal part of the MBD2 protein (Covalab, Villeurbanne, Lyon) (Perriaud et al. Curr. Pharm. Des 2013) using the ChIP Assay Kit (Merck Millipore, Saint-Quentin-en-Yvelines, France) as specified by the manufacturer’s instruction. Precipitated DNA was finally purified using NucleoSpin Gel and PCR Clean-up kit, (Macherey-Nagel) according to the manufacturer’s protocol “DNA clean-up of samples containing SDS”. DNA-end was repaired to overhang a 3'-dA, then adapters were ligated to the end DNA fragments. DNA fragments with proper size (usually 100-300bp, including adaptor sequence) were selected after PCR amplification.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
67634470
Reads aligned (%)
20.0
Duplicates removed (%)
76.4
Number of peaks
3413 (qval < 1E-05)

hg38

Number of total reads
67634470
Reads aligned (%)
21.6
Duplicates removed (%)
74.8
Number of peaks
3547 (qval < 1E-05)

Base call quality data from DBCLS SRA