Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
JUNB

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
keratinocytes
cell type
human neonatal keratincoytes
passage
Passage 3
chip antibody
JunB
chip antibody vendor
Cell signaling

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
primary keratinocytes cultured in eight 30-cm plates were scraped off the dish with PBS at about 60-80% confluence, and cross-linked with sequentially with 1% formaldehyde for 8 mins, then treated with 1.25M glycine for 5 min to stop crosslink. Cells were pelleted by centrifuging 5 min at 1500 rpm, and washed twice with PBS (1mM PMSF). Cell nuclei was isolated following cell lysis with ChIP lysis buffer and resuspended with complete RIPA buffer (Santa Cruz Biotechnology, Santa CruZ, CA) for DNA fragmentation by sonication with Branson Sonifier. The fragmented DNA underwent IP with the antibody against JunB (Cell Signaling Technology) followed by purification with MinElute DNA kit (Qiagen). 10 ng of the purified DNA was used for library construction with - the NEBNext® DNA library preparation kit (New England BioLabs).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
6706006
Reads aligned (%)
80.1
Duplicates removed (%)
1.4
Number of peaks
278 (qval < 1E-05)

hg38

Number of total reads
6706006
Reads aligned (%)
81.3
Duplicates removed (%)
0.8
Number of peaks
244 (qval < 1E-05)

Base call quality data from DBCLS SRA