Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Epidermis
Cell type
A-375
Primary Tissue
Skin
Tissue Diagnosis
Melanoma

Attributes by original data submitter

Sample

source_name
melanoma cell line
tissue
skin
cell type
melanoma cells
antibody
CTCF antibody (Cell Signaling Technology; #3418)
cell line
A375

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was sheared to around 150bp to 600bp using Covaris E220 machine and incubated with 6ul CTCF antibody (Cell Signaling Technology; #3418) overnight at 4°C with rotation. ChIP library was constructed using KAPA HTP library prep kit

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
44844911
Reads aligned (%)
39.7
Duplicates removed (%)
55.7
Number of peaks
8506 (qval < 1E-05)

hg38

Number of total reads
44844911
Reads aligned (%)
41.3
Duplicates removed (%)
54.4
Number of peaks
8672 (qval < 1E-05)

Base call quality data from DBCLS SRA