Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RBPJ

Cell type

Cell type Class
Epidermis
Cell type
Dermal fibroblast
NA
NA

Attributes by original data submitter

Sample

source_name
primary dermal fibroblasts
body site
abdomen skin
passage
4-6
antibodies
CSL (Cell Signaling RBPSUH Cat.No. 5313)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin from 10 milions fixed cells was fragmented to a size range of 100–300 bases with a Diagenode Bioruptor. Solubilized chromatin was immunoprecipitated with two different antibody against CSL. Antibody–chromatin complexes were pulled-down using protein A-sepharose, washed and then eluted. After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was extracted with phenol-chloroform, ethanol precipitated, and treated with RNase. ChIPed DNA was quantified by fluorometry on the Qubit system (Invitrogen). A total of 10 ng DNA were used for library preparation using NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina, as recommended by the manufacturer.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
27785243
Reads aligned (%)
11.3
Duplicates removed (%)
10.4
Number of peaks
1314 (qval < 1E-05)

hg38

Number of total reads
27785243
Reads aligned (%)
11.6
Duplicates removed (%)
9.3
Number of peaks
1388 (qval < 1E-05)

Base call quality data from DBCLS SRA