Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TP53

Cell type

Cell type Class
Epidermis
Cell type
Foreskin
MeSH Description
The double-layered skin fold that covers the GLANS PENIS, the head of the penis.

Attributes by original data submitter

Sample

source_name
Foreskin
treatment
Nutlin3A (5 uM)
antibody
p53

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For RNA-Seq: Total mRNA was extracted with E.Z.N.A. Total RNA kit (Omega; R6834-02) and Poly(A)+ RNA was isolated by double selection with poly-dT beads, using 2.5 mg total RNA, which is then followed by first- and second-strand synthesis For RNA-Seq: Libraries were prepared using NEXTflex Rapid Illumina DNA-Seq Library Prep Kit (Bioo Scientific). For ChIP-Seq: Cells were crosslinked at 80% confluency with 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with 125mM glycine and the resulting pellet was washed twice with cold PBS and lysed. Samples were subjected to sonication with Diagenode Bioruptor Plus for 40 cycles (30 sec on/off at high setting) for shearing chromatin to 150-500 bp average size. Immunoprecipitation reactions were performed with Diagenode IP-Star Compact Atuomated System with mentioned antibodies. Immunoprecipitated DNA was reverse-crosslinked at 65°C for 4 hours and then eluted from beads, purified using SPRI beads, and used to construct sequencing libraries. For ChIP-Seq: Libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
30401402
Reads aligned (%)
82.4
Duplicates removed (%)
10.6
Number of peaks
1896 (qval < 1E-05)

hg38

Number of total reads
30401402
Reads aligned (%)
85.1
Duplicates removed (%)
8.6
Number of peaks
2059 (qval < 1E-05)

Base call quality data from DBCLS SRA