Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ATF4

Cell type

Cell type Class
Digestive tract
Cell type
DLD-1
Primary Tissue
Colon
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
Human colon adenocarcinoma DLD-1 cell lines (ATCC CCL-221)
tissue
Human colon adenocarcinoma DLD-1 cell lines (ATCC CCL-221)
antibody
ATF4
myc status
activated
replicate
1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin fragments were prepared from DLD-1: MycER cells following 8hr of MYC activation (Vehicle or 4-OHT treatment). DNA was sonicated using Covaris 200 instrument at settings of Temp 5-9, PP200, DF 10, CB 200, 720sec. 50ug DNA was used for each ChIP. The following antibodies from Santa Cruz Biotechnology were used to perform ChIP at a concentration of 5ug: ATF4 (cat# sc-200x, lot# G0115, c-20), MYC (cat# sc-764, lot#D0413, N-262), Rabbit IgG (cat# sc-2027x, lot# G2516). Library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina #E7645S and NEBNext Multiplex Oligos for Illumina #E7335S according to manufacturer's instructions.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
32719278
Reads aligned (%)
89.7
Duplicates removed (%)
8.0
Number of peaks
1037 (qval < 1E-05)

hg38

Number of total reads
32719278
Reads aligned (%)
91.7
Duplicates removed (%)
6.7
Number of peaks
1089 (qval < 1E-05)

Base call quality data from DBCLS SRA