Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

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

Attributes by original data submitter

Sample

source_name
mouse embryonic stem cells
cell type
mouse embryonic stem cells (in 2i media)
transgene
mDuxCA
tag
3xHA-tag
condition
12hr dox-induction

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked in 1% formaldehyde for 10 minutes. Cells were then washed in PBS (x2) and resuspended in lysis buffer (10mM Tris,100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) to extract chromatin. Lysates were then sonicated using a BioRuptor, centrifuged to pellet cellular debris, and immunoprecipitated. After reversing crosslinks, libraries were prepped using the NEBnext DNA Library Prep Kit (NEB, E7370L). Adapter ligated DNA was size selected and purified using AMPure XP beads (Beckman Coulter, A63881) before sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
46119430
Reads aligned (%)
85.3
Duplicates removed (%)
15.0
Number of peaks
9695 (qval < 1E-05)

mm9

Number of total reads
46119430
Reads aligned (%)
85.3
Duplicates removed (%)
15.0
Number of peaks
9677 (qval < 1E-05)

Base call quality data from DBCLS SRA