Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTNNB1

Cell type

Cell type Class
Digestive tract
Cell type
SW 480
Primary Tissue
unresolved
Tissue Diagnosis
unresolved

Attributes by original data submitter

Sample

source_name
SW480
cell line
SW480
cell type
Colon cancer
passage
10 to 15
antibody
Anti-beta catenin(H102)
antibody vendor
Santa Cruz/sc-7199

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
After cross-linking, cells were scraped and sonicated utilizing Diagenode Bioruptor at High setting and cycling 30 seconds ON, 30 seconds OFF. Beta-catenin-DNA complexes were isolated with lab generated anti-beta-catenin antibody . ChIP DNA fragment ends were repaired and phosphorylated using Klenow, T4 DNA Polymerase and T4 Polynucleotide Kinase. Next, an ‘A’ base was added to the 3’ end of the blunted fragments, followed by ligation of Illumina adapters via T-A mediated ligation. The ligated products were size selected by gel purification and then PCR amplified using Illumina primers. The library size and concentration were determined using an Agilent Bioanalyzer.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
26311442
Reads aligned (%)
66.9
Duplicates removed (%)
28.3
Number of peaks
1029 (qval < 1E-05)

hg38

Number of total reads
26311442
Reads aligned (%)
67.9
Duplicates removed (%)
27.6
Number of peaks
929 (qval < 1E-05)

Base call quality data from DBCLS SRA