Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MBD2

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF-7 WT
antibody/details
BB2 (mouse monoclonal against TY1 epitope), Diagenode

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed for 10 minutes at room temperature by the addition of formaldehyde to a final concentration of 1%, after which glycine was added to a concentration of 100 mM. Cells were then washed twice with PBS and collected into 2 ml of lysis buffer (150 mM NaCl, 20 mM Tris pH 8.0, 2 mM EDTA, 1% triton X-100, protease inhibitor [complete EDTA free, Roche, 04 693 132 001], 100 mM PMSF). The lysate was sonicated to an average of 300-500bp fragments The resulting sonicate was centrifuged at 4000×g for 5 minutes, an aliquot of 10% retained for input and the remaining material transferred to a fresh tube. 5-10 ng DNA was subjected to end repair using Klenow DNA polymerase, T4 ligase and T4 polynucleotide kinase (T4 PNK). A 3′ protruding A base was generated using Taq polymerase and NEXTflex adapters were ligated. The DNA was subjected to 4 cycles PCR amplification using Kappa polymerase and purified DNA was loaded on E-gel for size selection (300 bp). The DNA was isolated, further amplified by PCR and used for cluster generation on the HiSeq2000 genome analyzer

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
27430048
Reads aligned (%)
23.4
Duplicates removed (%)
75.0
Number of peaks
313 (qval < 1E-05)

hg38

Number of total reads
27430048
Reads aligned (%)
25.4
Duplicates removed (%)
73.1
Number of peaks
195 (qval < 1E-05)

Base call quality data from DBCLS SRA