Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTNNB1

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC H1
NA
NA

Attributes by original data submitter

Sample

source_name
Embryonic Stem Cell H1
genotype
YAP-
treatment
Activin A
treatment_time
15h
antibody
beta-Catenin

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
PCR purification Kit (Qiaquick) from Qiagen was used to extract the DNA for ChIP-seq experiments. Quick RNA miniprep Plus from Zymo was used to extract the RNA for RNA-seq The ChIP DNA was end repaired and 5′ phosphorylated using T4 DNA Polymerase, Klenow, and T4 Polynucleotide Kinase (Enzymatics). Adaptor-ligated ChIP DNA fragments were subjected to 15 cycles of PCR amplification using Q5 polymerase (NEB). AMPure beads were used to purify DNA after each step (Beckman Coulter). ChIP fragments were sequenced in an Illumina HiSeq 2500 sequencer. RNA-seq libraries were performed using stranded LT mRNA kit from Illumina and sequenced in an Illumina HiSeq 4000 device.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
34353340
Reads aligned (%)
86.0
Duplicates removed (%)
7.2
Number of peaks
1914 (qval < 1E-05)

hg38

Number of total reads
34353340
Reads aligned (%)
88.2
Duplicates removed (%)
5.7
Number of peaks
2695 (qval < 1E-05)

Base call quality data from DBCLS SRA