Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

Cell type Class
Neural
Cell type
Glioblastoma stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
glioblastoma stem cells
cell line
3136
antibody
H3K27AC

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
5 million cells were crosslinked in 1% formaldehyde for 10 minutes, lysed, sonicated to ~500bp, and immunoprecipated using H3K27ac antibody (Active Motif 39133). In the case of tissue, 5-10mg of tissue was pulvarized in liquid nitrogen before cross-linking in the same manner as cell protocols (above) ChIP DNA was purified using the Qiagen PCR purification kit. Libraries were prepared according to manufacturers instructions using the Rubicon Thruplex DNA-seq kit Libraries were constructed using the DNA-seq kit from Rubicon Genomics and quantified using Picogreen

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
31310838
Reads aligned (%)
90.5
Duplicates removed (%)
12.1
Number of peaks
44190 (qval < 1E-05)

hg19

Number of total reads
31310838
Reads aligned (%)
90.2
Duplicates removed (%)
12.6
Number of peaks
43928 (qval < 1E-05)

Base call quality data from DBCLS SRA