Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Trp53

Cell type

Cell type Class
Adipocyte
Cell type
White adipocytes
NA
NA

Attributes by original data submitter

Sample

source_name
primary adipocytes
strain
C57BL/7
genotypes
p53178R/R (wild-type)
cell types
iWAT derived primary adipocytes
chip antibody
anti-p53 (Santa Cruz, FL393)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq samples, primary adipocytes were cross-linked with 1.5% formaldehyde for 10 min, and the nuclear extracts were sonicated and immunoprecipitated with anti-p53 (FL393, Santa Cruz). Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA sample prep kit (Cat no. FC-121-2001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15-18 cycles and library fragments of 200-400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 3000

mm10

Number of total reads
67898960
Reads aligned (%)
96.0
Duplicates removed (%)
20.0
Number of peaks
4862 (qval < 1E-05)

mm9

Number of total reads
67898960
Reads aligned (%)
95.7
Duplicates removed (%)
19.9
Number of peaks
4874 (qval < 1E-05)

Base call quality data from DBCLS SRA