Curated Sample Data


Genome
mm9
Antigen Class
Histone
Antigen
H3S10ph
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
Embryonic stem cells
cell type
Embryonic stem cells
strain
129P2/Ola
antibody
ab14955, abcam

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For each sample, 1 x 10^6 cells were cross-linked with 1% PFA and cell nuclei were prepared using a swelling buffer (25 mM Hepes, pH 7.8, 1 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT). For histone modifiacations, chromatin was sheared to mononucleosomal fragments. For RNA-seq RNA was extracted and treated with RiboZero followed by DNaseI digestion. Libraries were prepared according to Illumina standard protocols with internal barcodes.

Platform Information


instrument_model
Illumina HiSeq 2000

External Database Query

Logs in read processing pipeline


Number of total reads
24238695
Reads aligned (%)
89.4
Duplicates removed (%)
84.5
Number of peaks
5038 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA