Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Digestive tract
Cell type
RKO
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
RKO
cell line
RKO
cell type
colorectal cancer cells
treatment
conjugated NCD38 with Py-Im polyamide P4_NCD38
antibody
Histone H3K4me3 antibody [pAb] (#ab7766, Abcam, Lot#GR160184-2)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP samples were purified by QIAquick PCR purification kit (Qiagen, Hilden, Germany) and total RNAs were collected using RNeasy (Invitrogen, Carlsbad, CA) Libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) for ChIP-seq. TruSeq Stranded mRNA Sample Prep Kit (Illumina) were used for RNA-seq following the manufacturer's protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 1500

hg38

Number of total reads
27637753
Reads aligned (%)
99.2
Duplicates removed (%)
18.4
Number of peaks
25214 (qval < 1E-05)

hg19

Number of total reads
27637753
Reads aligned (%)
98.7
Duplicates removed (%)
18.8
Number of peaks
25312 (qval < 1E-05)

Base call quality data from DBCLS SRA