Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

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
GM12878 cells
biomaterial_provider
CC
cell line
GM12878
chip antibody
H3K27ac (Abcam ab4729, Lot: 509313)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: Cells and tissues were cross-linked with 1% formaldehyde for 15 min. Glycine (0.625 M) was added to quench excess formaldehyde. Cells were washed in cold PBS and spun down (3,000 r.p.m. (800g) for 10 min at 4 °C; Kubota 3500). The pellet was  resuspended  in FA lysis buffer and incubated for 15minutes (0.25% Triton X-100, 10 mM EDTA, 10 mM Tris HCl [pH 8.0], 100 mM NaCl, Roche 1X cOmplete protease inhibitor). Nuclei were extracted (3,000 r.p.m. for 10 min at 4 °C; Kubota 3500) and resuspended in 300 μl SDS lysis buffer (1% SDS, 1% Triton X-100, 2 mM EDTA, 50 mM HEPES-KOH [pH 7.5], 0.1% Na dodecyl sulfate, Roche 1X cOmplete protease inhibitor). After 15 min incubation, chromatin was fragmented to an average size of 200–300 bp (Bioruptor Next gen, Diagenode). Cellular debris was removed by centrifuging at 15,000 r.p.m. at 4 °C (Kubota 3500). Nuclear lysates were diluted (1:10) with a dilution buffer (1% Triton X-100, 2 mM EDTA, 50 mM HEPES-KOH [pH 7.5], 0.1% Na dodecyl sulfate, Roche 1X cOmplete protease inhibitor).   Chromatin immunoprecipitation (ChIP)  was done coupled to 50 μl protein G Dynabeads (Invitrogen) overnight. The antibodies used for ChIP were : H3K4me2 (Abcam ab32356, lot 780430)), H3K4me1(Abcam:ab8895, lot 718019), H3K27ac( Abcam ab4729, lot 509313), H3K27me3 ( Millipore 07-449, lot DAM1588246 ), PolII ( Abcam ab5131, lot 536530) , H2BK20ac ( Abcam ab52988, lot 527003). After ChIP overnight, beads were washed, and protein-DNA complexes were eluted with  elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl [pH 8]).  Protease treatment and de-cross-linking was done at 65 °C overnight., DNA was extracted using phenol/chloroform and purified by ethanol precipitation. ChIP material was used for library preparation using the Biooscientific library preparation kit with the following modification. The provided adapters were diluted down 40-fold in order to prevent adapter dimer formation that would affect enrichment. Libraries were then enriched for 15 cycles with PFX polymerase (Invitrogen) followed by gel size selection (300-500bp).

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg38

Number of total reads
14425372
Reads aligned (%)
92.6
Duplicates removed (%)
9.6
Number of peaks
26797 (qval < 1E-05)

hg19

Number of total reads
14425372
Reads aligned (%)
92.2
Duplicates removed (%)
9.6
Number of peaks
27453 (qval < 1E-05)

Base call quality data from DBCLS SRA