Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

Cell type Class
Breast
Cell type
SUM 159PT
Primary Tissue
Breast
Tissue Diagnosis
Anaplastic Carcinoma

Attributes by original data submitter

Sample

source_name
SUM159R
cell line
SUM159R
chip antibody
H3K27AC (Abcam, catalog# ab4729, lot# GR184557-1)
drug treatment
JQ1
duration
3 hour

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
67802395
Reads aligned (%)
92.6
Duplicates removed (%)
49.3
Number of peaks
67746 (qval < 1E-05)

hg19

Number of total reads
67802395
Reads aligned (%)
92.4
Duplicates removed (%)
49.9
Number of peaks
67350 (qval < 1E-05)

Base call quality data from DBCLS SRA