Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Epidermis
Cell type
Melanoma
MeSH Description
A malignant neoplasm derived from cells that are capable of forming melanin, which may occur in the skin of any part of the body, in the eye, or, rarely, in the mucous membranes of the genitalia, anus, oral cavity, or other sites. It occurs mostly in adults and may originate de novo or from a pigmented nevus or malignant lentigo. Melanomas frequently metastasize widely, and the regional lymph nodes, liver, lungs, and brain are likely to be involved. The incidence of malignant skin melanomas is rising rapidly in all parts of the world. (Stedman, 25th ed; from Rook et al., Textbook of Dermatology, 4th ed, p2445)

Attributes by original data submitter

Sample

source_name
melanoma cells
cell type
ocular melanoma cells
chip antibody
CTCF

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using CTCF antibody(Active Motif, Catalog No: 61311). Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg19

Number of total reads
16243742
Reads aligned (%)
0.0
Duplicates removed (%)
18.7
Number of peaks
0 (qval < 1E-05)

hg38

Number of total reads
16243742
Reads aligned (%)
0.0
Duplicates removed (%)
18.1
Number of peaks
0 (qval < 1E-05)

Base call quality data from DBCLS SRA