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 TTE-MBD2
genetic manipulation
MCF7 cell line has been stably trasfected with TTE-MBD2 construct.
antibody/details
Rabbit anti-MBD2 Antibody, Bethyl Laboratories , (A301-632)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were trypsinized and re-suspended with PBS to a final concentration of 8x106 cells/ 500 μl PBS. Cell suspensions were crosslinked with 1.5mM DSG (disuccinimidyl glutarate, Thermo, #20593) for 45' at room temperature with gentle rotation. After two washes with 500 μl PBS, cell pellets were re-suspended in 1ml PBS and 1% formaldehyde was added for 10' at room temperature. Cross-linking was quenched with 125mM glycine and after two times ice-cold PBS washes, pellets were resuspended in 270 μl lysis buffer (50mM Tris pH8.0, 1%SDS, 10mMEDTA protease inhibitor) and incubated 5' on ice. Sonication was performed for 15'-20' with Bioruptor sonicator (NGS, Diagenode) and lysates were centrifuged at 13000rpm 4°C, for 5min. 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
42797239
Reads aligned (%)
90.3
Duplicates removed (%)
7.8
Number of peaks
3571 (qval < 1E-05)

hg38

Number of total reads
42797239
Reads aligned (%)
93.4
Duplicates removed (%)
5.6
Number of peaks
3554 (qval < 1E-05)

Base call quality data from DBCLS SRA