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
TT2 ESCs
strain
C57Bl6/CBA
cell type
embryonic stem cell
genotype
WT
Sex
male
chip protocol
Crosslinked MNAse
chip antibody
H3S10ph (CMA311)

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For crosslinked MNase ChIP, cells were crosslinked (1% formaldehyde, 10mins) and digested with microccocal nuclease, nuclei were then isolated and flash frozen. For native ChIP, flash frozen cell pellets were lysed with hypotonic buffer and digested with micrococcal nuclease. Protein:DNA complexes were immunoprecipitated with specific antibodies pre-bound to protein A/G or goat anti-mouse IgG magnetic beads. Eluted DNA underwent crosslink reversal, if necessary, were RNAse treated followed by phenol:choloroform cleanup. Cells harvested and flash frozen using liquid nitrogen. RNA was then extracted using Sigma GenElute Mammalian Total RNA Extraction Kit RNA-seq libraries were prepared from mRNA as described in Morin et al from 10ug of DnaseI treated total RNA (Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh T, McDonald H, Varhol R, Jones S, Marra M: Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. BioTechniques 2008, 45:81-94.) Adaptor ligation based library construction for paired-end Illumina sequencing

Platform Information


instrument_model
Illumina HiSeq 2000

External Database Query

Logs in read processing pipeline


Number of total reads
22927790
Reads aligned (%)
96.7
Duplicates removed (%)
5.9
Number of peaks
108 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA