Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

Cell type Class
Blood
Cell type
DLBCL
NA
NA

Attributes by original data submitter

Sample

source_name
Diffuse large B-cell lymphoma
cell strain
U2932
chip antibody
H3K27ac (Active Motif, 39133, lot 31814008)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
34115913
Reads aligned (%)
96.7
Duplicates removed (%)
7.5
Number of peaks
21974 (qval < 1E-05)

hg19

Number of total reads
34115913
Reads aligned (%)
96.4
Duplicates removed (%)
7.7
Number of peaks
21983 (qval < 1E-05)

Base call quality data from DBCLS SRA