Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PPARG

Cell type

Cell type Class
Adipocyte
Cell type
Adipose Tissue, White
MeSH Description
Fatty tissue composed of WHITE ADIPOCYTES and generally found directly under the skin (SUBCUTANEOUS FAT) and around the internal organs (ABDOMINAL FAT). It has less vascularization and less coloration than the BROWN FAT. White fat provides heat insulation, mechanical cushion, and source of energy.

Attributes by original data submitter

Sample

source_name
RS_070
experiment type
PPARG ChIP-seq
tissue
SQ White Adipose Tissue
chip antibody
anti-PPAR? antibody
chip antibody vendor
Santa Cruz Biotechnologies

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated from either cells or minced tissue and Transcription Factor-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (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 cycles and library fragments of ~250 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 2000

hg19

Number of total reads
20062019
Reads aligned (%)
51.4
Duplicates removed (%)
47.0
Number of peaks
802 (qval < 1E-05)

hg38

Number of total reads
20062019
Reads aligned (%)
52.7
Duplicates removed (%)
46.0
Number of peaks
884 (qval < 1E-05)

Base call quality data from DBCLS SRA