Curated Sample Data


Genome
mm9
Antigen Class
TFs and others
Antigen
Nanog
Cell type Class
Pluripotent stem cell
Cell type
Embryonic Stem Cells

Cell type information


MeSH Description
Cells derived from the BLASTOCYST INNER CELL MASS which forms before implantation in the uterine wall. They retain the ability to divide, proliferate and provide progenitor cells that can differentiate into specialized cells.

Attributes by Original Data Submitter


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

Metadata from Sequence Read Archive

Library Description


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)

Platform Information


instrument_model
Illumina HiSeq 1000

External Database Query

Logs in read processing pipeline


Number of total reads
3085119
Reads aligned (%)
0.0
Duplicates removed (%)
9.9
Number of peaks
0 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA