Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCFL

Cell type

Cell type Class
Epidermis
Cell type
NHDF
Primary Tissue
Skin
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
Human Normal Dermal Fibroblasts
cell line
NHDF
chip antibody
custom mouse monoclonal BORIS (characterized in PMID: 21659515)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
After overnight incubation with DiaMag magnetic beads (Diagenode, Inc.) and CTCF or BORIS monoclonal or polyclonal antibodies (characterized and described by PMID:15731119; PMID: 21659515; PMID:20231363), precipitated chromatin was then washed, decrosslinked, and digested with proteinase K. The resulting DNA was purified using phenol/chloroform/isoamyl alcohol. DNA concentration was assessed with Quant‐it PicoGreen dsDNA kit (Invitrogen) and 5–10 ng was used to generate sequencing libraries. TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA). RNA-seq libraries were prepared using either Ion Total RNA-seq v2 kit or TruSeq Stranded RNA LT Kit (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
19277565
Reads aligned (%)
37.0
Duplicates removed (%)
19.8
Number of peaks
860 (qval < 1E-05)

hg38

Number of total reads
19277565
Reads aligned (%)
37.9
Duplicates removed (%)
18.7
Number of peaks
675 (qval < 1E-05)

Base call quality data from DBCLS SRA