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 derived neural cells
NA
NA

Attributes by original data submitter

Sample

source_name
Neural epithelial cells
cell type
Human ES-derived neural epithelial cells
genotype/variation
SOX21-/-
time point
Day 5
chip antibody
b-catenin (BD Biosciences, 610154)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Neural epithelial cell lysates were clarified from sonicated nuclei and SOX21 complexes or b-catenin-DNA complexes were immunoprecipitated with SOX21 antibody (R&D AF3538) or b-catenin antibody (BD Biosciences, 610154), respectively. Protein A and G Magnetic Dynabeads were used to capture antibody-bound protein-DNA complexes. The ChIP-enriched DNA samples were treated with end-repair of the DNA, adding “A” bases to the DNA, ligating sequencing adapters to DNA fragments, amplifying adapter-modified DNA by PCR and gel purification for ChIPseq using NEBNext Ultra DNA Library Prep Kit for Illumina. Purified libraries were sequenced on Illumina HiSeq X-ten platforms.

Sequencing Platform

instrument_model
HiSeq X Ten

hg19

Number of total reads
20275775
Reads aligned (%)
180.5
Duplicates removed (%)
6.9
Number of peaks
325 (qval < 1E-05)

hg38

Number of total reads
20275775
Reads aligned (%)
182.8
Duplicates removed (%)
6.8
Number of peaks
861 (qval < 1E-05)

Base call quality data from DBCLS SRA