Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ATR

Cell type

Cell type Class
Digestive tract
Cell type
HCT 116
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
HCT-116 cells
cell line
HCT-116
cell type
Colorectal cancer cell line
genotype/variation
DNA2 KO
chip antibody
Rabbit phosphor-ATR antibody (Genetex, GTX128145)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For CHIP-DNA2, lysates were clarified from sonicated nuclei and DNA2-DNA complexes were isolated with antibody. For collection of BrdU negative DNA, separation of BrdU-labeled DNA from unlabeled DNA was done as previously described (Roux-Michollet et al, 2010; Viggiani et al, 2010). Briefly, 20 µL of DNA at ~20 ng/µL in PBS was heat denatured at 100 ºC for 1 min, and transferred to an ice-ethanol bath for 30-50 s to flash freeze. Tubes of DNA were then thawed completely at RT (less than 3 min), mixed with 2 μL of a BrdU antibody (BD Biosciences, cat# 347580), and incubated at RT for 30-40 min in the dark with occasional mixing. The BrdU-labeled DNA, bound with antibody, was then isolated with 20 µL of prepared Dynabeads Sheep anti-Mouse IgG (Thermo Scientific cat# 11031). The BrdU-negative DNA was collected by sequencing. Libraries were constructed using Kapa's HyperPlus Kits

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
48319172
Reads aligned (%)
72.3
Duplicates removed (%)
6.0
Number of peaks
1651 (qval < 1E-05)

hg38

Number of total reads
48319172
Reads aligned (%)
74.0
Duplicates removed (%)
4.8
Number of peaks
1487 (qval < 1E-05)

Base call quality data from DBCLS SRA