Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Epidermis
Cell type
COLO 679
Primary Tissue
Skin
Tissue Diagnosis
Melanoma

Attributes by original data submitter

Sample

source_name
human melanoma cell lines
cell line
COLO679
cell type
melanoma
passages
long term culture
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed using the methods of T. I. Lee, S. E. Johnstone, R. A. Young, Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc. 1, 729–748 (2006). Libraries were prepared using the NEBNext Multiplex Oligos for Illumina kit (NEB) and run on an Illumina Hi-Seq2000.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
29283214
Reads aligned (%)
99.5
Duplicates removed (%)
1.6
Number of peaks
682 (qval < 1E-05)

hg19

Number of total reads
29283214
Reads aligned (%)
99.0
Duplicates removed (%)
2.5
Number of peaks
756 (qval < 1E-05)

Base call quality data from DBCLS SRA