Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KMT2A

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC H9
NA
NA

Attributes by original data submitter

Sample

source_name
H9
cell line
H9
cell type
Human ES
genotype
WT
treatment
EPZ+VTP
chip antibody
MLL1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 2mM DSG (Theromo Scientific) for 30min at room temperature followed by cross-linking with 1% formaldehyde (methanol free) for 15 min at room temperature, and cross-linking was stopped by the addition of 0.125 M glycine. Cells were lysed in 1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0, and protease inhibitors. Lysates were sonicated in a Covaris ultrasonicator to achieve a mean DNA fragment size of 500 bp. Samples were diluted 1:10 in modified RIPA buffer (1% Triton X-100, 0.1% deoxycholate, 90 mM NaCl, 10 mM Tris-HCl, pH 8.0, and protease inhibitors) and incubated rotating with antibody for a minimum of 12 h at 4 °C. Protein A Dynabeads (Life Technologies) were used to bind the antibody and associated chromatin. After washing and elution from the beads, samples were reverse cross-linked overnight and purified with MinElute PCR purification kit (Qiagen). Sequencing libraries were prepared from eluted DNA using Rubicon ThruPLEX DNA-seq kit.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
31170812
Reads aligned (%)
92.5
Duplicates removed (%)
5.8
Number of peaks
10986 (qval < 1E-05)

hg19

Number of total reads
31170812
Reads aligned (%)
92.1
Duplicates removed (%)
6.6
Number of peaks
10856 (qval < 1E-05)

Base call quality data from DBCLS SRA