Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H4K5K8ac

Cell type

Cell type Class
Blood
Cell type
GM12878
Tissue
blood
Lineage
mesoderm
Description
B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

Attributes by original data submitter

Sample

source_name
lymphoblastoid cell line
biomaterial_provider
GM12878
cell line
GM12878
treatment
-
antibody
H4K5acK8ac
antibody type
mouse monoclonal

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. The crosslink reaction was stopped by addition of Glycin at the final concentration of 0.2M. H23 Chromatin extract was prepared as follows: the cell pellets were dissolved and incubated in the ice-cold 0.1% SDS lysis buffer (50 mM Hepes KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, 0.1% SDS, protease inhibitors) for 10 min on a rotation at 4°C. Following centrifugation, the cells were incubated in the ice-cold second lysis buffer (10 mM Tris-CL pH 8.0, 200 mM NaCl, 1 mM EDTA pH. 8.0, 0.5 mM EGTA pH 8.0, protease inhibitors) as described above. The cells were then dissolved in 0.5% SDS sonication buffer (3.106 cells per 135mg sonication buffer), directed to chromatin fragmentation by Covaris for 10 min ChIP-seq library for sequencing was prepared as the manufacture's protocol: Mondrian™ SP+ Library Preparation (NuGen)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
21047453
Reads aligned (%)
99.8
Duplicates removed (%)
15.1
Number of peaks
19569 (qval < 1E-05)

hg19

Number of total reads
21047453
Reads aligned (%)
99.8
Duplicates removed (%)
15.3
Number of peaks
19528 (qval < 1E-05)

Base call quality data from DBCLS SRA