Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Nr0b1

Cell type

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

Attributes by original data submitter

Sample

source_name
bioDax1 ChIP DNA from ES cells
strain background
129/Sv
cell line
J1
cell type
mouse embryonic stem cells
genotype/variation
expressing Flag-bio tagged Dax1
chip beads
Dynabeads MyOne Streptavidin T1
chip beads vendor
Invitrogen

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The Flag-bio tagged mouse ES cells were fixed in 1% formaldehyde for 7 minutes at room temperature. The formaldehyde was quenched using 2.5M glycine before harvest for extract preparation. Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with size of 500-800bp were immunoprecipitated using Streptavidin beads (Dynabeads MyOne Streptavidin T1), and 2% SDS was applied for one of the washing steps. massive parallel sequencing (bioChIP-Seq)

Sequencing Platform

instrument_model
Illumina HiSeq 1000

mm10

Number of total reads
45628787
Reads aligned (%)
62.6
Duplicates removed (%)
59.7
Number of peaks
13599 (qval < 1E-05)

mm9

Number of total reads
45628787
Reads aligned (%)
62.5
Duplicates removed (%)
59.8
Number of peaks
13527 (qval < 1E-05)

Base call quality data from DBCLS SRA