Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Digestive tract
Cell type
Colorectal cancer cell lines
NA
NA

Attributes by original data submitter

Sample

source_name
CRC cell line
tissue
colorectal cancer cell line
cell line
V1058
chip antibody
rabbit anti-H3K4me1 (Abcam #8895)

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
44274163
Reads aligned (%)
97.9
Duplicates removed (%)
3.7
Number of peaks
2293 (qval < 1E-05)

hg19

Number of total reads
44274163
Reads aligned (%)
97.6
Duplicates removed (%)
4.1
Number of peaks
2244 (qval < 1E-05)

Base call quality data from DBCLS SRA