Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

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
CRC cell line
tissue
colorectal cancer cell line
cell line
SW480

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-Seq, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For DNase Hypersensitivity, nuclei were isolated and treated with DNase I. For RNA-Seq samples, cells were lysed and RNA extracted with TRIzol according to the manufacturer’s protocol. ChIP-Seq libraries were prepared with NEB reagents as previously described. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers and library fragments of ~250 bp were band isolated from an agarose gel. DNase Hypersensitivity libraries were prepared as previously described. Briefly, DNase I treated DNA was blunt-ended. DNA fragments were ligated to biotinylated linkers and digested with MmeI, producing 2 bp overhangs for ligation with a second linker or Illumina adapters. DNA was then PCR amplified and library fragments of ~86 bp were band isolated from a gel. RNA libraries were prepared for sequencing using standard Illumina protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
61135527
Reads aligned (%)
96.8
Duplicates removed (%)
7.8
Number of peaks
1259 (qval < 1E-05)

hg19

Number of total reads
61135527
Reads aligned (%)
95.8
Duplicates removed (%)
9.4
Number of peaks
1331 (qval < 1E-05)

Base call quality data from DBCLS SRA