Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ORC2

Cell type

Cell type Class
Blood
Cell type
K-562
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Chronic Myelogenous

Attributes by original data submitter

Sample

source_name
genomic DNA
cell line
K562 cell
chip antibody
ORC2 antibody (Santa Cruz, sc-28742)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
After pre-clearing with protein A sepharose beads (4C for 1 hours), the chromatin from an equivalent of 5x107 cells was used for immunoprecipitation with an ORC2 antibody (Santa Cruz, sc-28742 or BD Biosciences, bd-6875) or IgG as a control. After 4C overnight incubation, beads were washed, eluted in buffer E (25mM Tris-HCl pH 7.5; 5mM EDTA; 0.5% SDS) and cross-links reversed at 65C with proteinase K for 6 hours. ChIP libraries were created using 15 cycles of amplification according to the Illumina manufacturer protocol. Libraries were run on a 2% agarose gel, and the 150-450 bp fraction was extracted and purified using DNA gel extraction kit (QIAGEN). To estimate the yield of library and its relative amplification value, library DNA was quantitated using a Nanodrop. Quality of the library was access by qPCR monitoring at known origins (see primers above).

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
8597928
Reads aligned (%)
84.5
Duplicates removed (%)
5.8
Number of peaks
7741 (qval < 1E-05)

hg38

Number of total reads
8597928
Reads aligned (%)
85.1
Duplicates removed (%)
5.5
Number of peaks
7720 (qval < 1E-05)

Base call quality data from DBCLS SRA