Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KDM4A

Cell type

Cell type Class
Breast
Cell type
BCSC1
NA
NA

Attributes by original data submitter

Sample

source_name
ChIP_KDM4A
cell line
breast triple negative tumor cell line BCSC1
treatment
shRNA control
chip antibody
KDM4A (Schuele Lab; #5766, lot 21110)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Metzger, E., et al. Phosphorylation of histone H3 at threonine 11 establishes a novel chromatin mark for transcriptional regulation. Nat Cell Biol 10, 53-60 (2008), Drosophila Spike in Chromatin was added in H3K9me3 control and H3K9me3 (i) samples. Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the hg19 reference genome using bowtie 2

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
31939783
Reads aligned (%)
110.8
Duplicates removed (%)
16.7
Number of peaks
37198 (qval < 1E-05)

hg38

Number of total reads
31939783
Reads aligned (%)
111.3
Duplicates removed (%)
16.6
Number of peaks
36979 (qval < 1E-05)

Base call quality data from DBCLS SRA