Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTBP2

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
MCF7
cell line
MCF7
cell type
breast cancer cell line
genotype/variation
TRPS1 KO
yap 5sa induced
No
chip antibody
CtBP2 (BD Bioscience, Cat# 612044)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked with 1% formaldehyde for 10 min at RT. Nuclei were extracted using hypotonic buffer (20 mM Tris, pH 7.4, 2 mM MgCl2, 5% glycerol) and lysed with ChIP lysis buffer (20 mM Tris pH 7.4, 150 mM NaCl, 1% NP40, 0.5% DOC, 0.1% SDS, 1 mM EDTA). Chromatin was sonicated to obtain fragments of 200 bp. Equilibration of beads (Dynabeads, Thermo Scientific) with antibodies (2 μg for ChIP, 10 μg for ChIP-Seq) was performed overnight, following immunoprecipitation of chromatin for 6h. After extensive washing, bound chromatin was eluted using ChIP elution buffer (50 M Tris, pH 8.0, 1 mM EDTA, 1% SDS, 50 mM NaHCO3) and de-crosslinked and RNase A/Proteinase K (Roth) digested over night. DNA was purified by phenol/chloroform extraction and ethanol precipitation. ChIP-Seq libraries were generated according to the manufacturer's protocol (NEBNext Ultra II DNA Library Prep Kit for Illumina, NEB) using Dual Index Primers (NEBNext Multiplex Oligos for Illumina, NEB). The number of PCR cycles varied between 9-12 PCR cycles. The optimal PCR cycle number was determined beforehand using a qPCR machine with 10% of the material used for the final amplification.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
21499537
Reads aligned (%)
91.9
Duplicates removed (%)
5.8
Number of peaks
1655 (qval < 1E-05)

hg38

Number of total reads
21499537
Reads aligned (%)
93.8
Duplicates removed (%)
4.6
Number of peaks
1688 (qval < 1E-05)

Base call quality data from DBCLS SRA