Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Pluripotent stem cell
Cell type
iPS cells
NA
NA

Attributes by original data submitter

Sample

source_name
single-cell CVB derived hiPSC#2 subline (genome editing: PSEN1 deltaE9 +/-, IIA11)
cell line
Craig Venter-B (CVB) hiPSC subline

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 2mM disuccinimidyl glutarate (DSG) for 45 mins and 1% formaldehyde for 10mins, and followed by glycine for 5 mins. Chromatin DNA was sheared to 200–500 bp average in size by sonication and chromatin was immunoprecipitated with antibodies. Protein A/G beads Sigma were added and incubated overnight at 4°C. After washing and elution, the protein–DNA complex was reverse-crosslinked by heating at 65°C, and immunoprecipitated DNA was purified by using QIAquick Spin column. ChIP-seq libraries were prepared using the KAPA Library Preparation Kit (KK8201)

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
31067638
Reads aligned (%)
90.0
Duplicates removed (%)
3.7
Number of peaks
32224 (qval < 1E-05)

hg19

Number of total reads
31067638
Reads aligned (%)
89.7
Duplicates removed (%)
4.1
Number of peaks
32207 (qval < 1E-05)

Base call quality data from DBCLS SRA