Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
YAP1

Cell type

Cell type Class
Gonad
Cell type
OVCAR-5
Primary Tissue
Ovary
Site of Extraction
Ascites
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
OVCAR5 cell line
cell type
Ovarian cancer cell
cell line
OVCAR5
antibody
YAP (H125)X
vendor
Santa Cruz Biotechnologies
catalog number
sc15407
lot number
c-1904

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Formaldehyde fixed chromatin was isolated from cells and YAP1 bound chromatin was purified using YAP1 antibody using standard Chromatin IP method. Libraries were prepared using NEB reagents as described earlier (Garber et al 2012). 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 12 cycles and library fragments of ~300-500 bp (insert plus adaptor and PCR primer sequences) were size selected by SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
24743584
Reads aligned (%)
34.9
Duplicates removed (%)
18.2
Number of peaks
613 (qval < 1E-05)

hg38

Number of total reads
24743584
Reads aligned (%)
35.3
Duplicates removed (%)
17.6
Number of peaks
569 (qval < 1E-05)

Base call quality data from DBCLS SRA