Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA

Attributes by original data submitter

Sample

source_name
ESC time-ChIP input (for replicates 2 and 3)
cell type
ESC
strain
A2lox.Cre (derived from E14)
replicate
2
time point
input

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were harvested and nuclei isolated. Nuclei were digested with 120-140U MNase in the presence of 3mM CaCl2 for 20min at 25°C. Reactions were stopped and the MNase digested chromatin was centrifuged at 12,000g for 5min. The resulting supernatant was added to 15µl streptavidin magnetic beads and incubated for 1h at 4°C. Beads were washed and DNA eluted and purified according to standard protocols. Sequencing libraries were prepared as described in Bowman et al. (Bowman et al., 2013).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
68432671
Reads aligned (%)
98.4
Duplicates removed (%)
9.2
Number of peaks
158 (qval < 1E-05)

mm9

Number of total reads
68432671
Reads aligned (%)
98.3
Duplicates removed (%)
9.4
Number of peaks
145 (qval < 1E-05)

Base call quality data from DBCLS SRA