Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RBPJ

Cell type

Cell type Class
Epidermis
Cell type
Keratinocytes
MeSH Description
Epidermal cells which synthesize keratin and undergo characteristic changes as they move upward from the basal layers of the epidermis to the cornified (horny) layer of the skin. Successive stages of differentiation of the keratinocytes forming the epidermal layers are basal cell, spinous or prickle cell, and the granular cell.

Attributes by original data submitter

Sample

source_name
HKC
chip antibody
CSL antibody

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
DNA was immunoprecipitated from 5 x 10e6 HKCs using 10 μl of CSL antibody per 10e6 cells, followed by quantification by fluorometry on a Qubit system (Invitrogen). A total of 10 ng of DNA was used for library preparation using NEBNext ChIP-Seq Library Prep Kit (Illumina) according to manufacturer’s recommendation.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
55570821
Reads aligned (%)
54.7
Duplicates removed (%)
42.8
Number of peaks
1365 (qval < 1E-05)

hg38

Number of total reads
55570821
Reads aligned (%)
56.6
Duplicates removed (%)
41.2
Number of peaks
1725 (qval < 1E-05)

Base call quality data from DBCLS SRA