Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Digestive tract
Cell type
LoVo
Primary Tissue
Colon
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
CRC cell line
sample type
LoVo cells
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. 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.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
101577409
Reads aligned (%)
87.8
Duplicates removed (%)
8.1
Number of peaks
2567 (qval < 1E-05)

hg19

Number of total reads
101577409
Reads aligned (%)
87.0
Duplicates removed (%)
9.7
Number of peaks
1952 (qval < 1E-05)

Base call quality data from DBCLS SRA