Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Blood
Cell type
HAP1
NA
NA

Attributes by original data submitter

Sample

source_name
HAP1
cell line
HAP1
treatment
3h EBSS
chip-antibody
Rabbit anti-histone H3 trimethyl K4 (39159; Active Motif)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells from two independent biological replicates were crosslinked in 1% formaldehyde, 5 mM Hepes-KOH (pH 7.5), 10 mM NaCl, 0.1 mM EDTA, and 50 µM EGTA and after 10 min crosslinking was stopped by adding 0.1 M glycine. Nuclei were isolated in 50 mM Tris (pH 7.5), 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, and 1% Triton X-100 and lysed in 20 mM Tris (pH 7.5), 150 mM NaCl, 2 mM EDTA, 1% NP-40, 0.3% SDS. Lysates were reduspended in 20 mM Tris (pH 8.0), 150 mM NaCl, 2 mM EDTA, 1% X-100 and sonicated using Covaris (8 min, maximum output). Sheared DNA was incubated overnight with the indicated antibodies pre-coupled to protein A/G magnetic beads. Cells were washed and crosslinking was reversed by adding 1% SDS, 100 mM NaHCO3, 200 mM NaCl, and 300 mg/ml proteinase K. DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research). Endrepair, a-tailing, and ligation of sequence adaptors was done using Truseq nano DNA sample preparation kit (Illumina). Samples were PCR amplified and barcoded libraries were sequenced 75 bp single-end on Illumina NextSeq500 sequencer.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
13192623
Reads aligned (%)
95.8
Duplicates removed (%)
14.8
Number of peaks
19173 (qval < 1E-05)

hg19

Number of total reads
13192623
Reads aligned (%)
95.7
Duplicates removed (%)
14.9
Number of peaks
19159 (qval < 1E-05)

Base call quality data from DBCLS SRA