Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KMT2D

Cell type

Cell type Class
Breast
Cell type
T-47D
Primary Tissue
Breast
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by original data submitter

Sample

source_name
Breast Cancer Cell
cell line
T47D cell
passages
5 to 10
chip antibody
Anti-KMT2D, HPA035977, Sigma
treatment
DMSO

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were lysed and sonicated leading to a DNA average size of 200bp. Protein G dynabeads were pre-incubated with 5μg of KMT2D antibody (HPA035977, Sigma) with pre cleared chromatin. The complexes were reverse cross-linked and DNA was purified. Due to low enrichment due to antibody lot issues, ChIP-seq libraries were prepared using the total 5 ng of DNA and Illumina's TruSeq ChIP sample prep.Libraries were validated using the Agient Technologies 2100 Bioanalyzer and Qubit high sensitivity assay.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
78084815
Reads aligned (%)
80.6
Duplicates removed (%)
12.6
Number of peaks
2082 (qval < 1E-05)

hg38

Number of total reads
78084815
Reads aligned (%)
82.7
Duplicates removed (%)
10.9
Number of peaks
2308 (qval < 1E-05)

Base call quality data from DBCLS SRA