Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27me3

Cell type

Cell type Class
Embryo
Cell type
Primordial germ cells
NA
NA

Attributes by original data submitter

Sample

source_name
E15.5 fetal male germ cells
strain
129T2svj/C57bl6
cell type
fetal germ cells
gender
male
developmental stage
embryonic day 15.5
genotype
Embryonic Ectoderm Development (Eed) wild type
antibody
H3K27me3

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were collected via FACS using Oct4GFP expression to identify germ cells. Approximately 10,000 germ cells were FACS purified from individual Eedwt/wt (n=4) and Eedhypo/hypo (n=4) embryos and ChIP performed as described [81, 82] with minor alterations. Briefly, cells were cross-linked in 1% Formaldehyde/PBS for 5 min before adding Glycine/PBS at a final concentration of 125mM. Cells were pelleted and washed in PBS and stored -80°C. Libraries were prepared from using the Ovation Ultralow System V2 using Nugen protocol M01379v1. Each library was quantitated using a Qubit instrument and the DNA size profile determined using an Agilent Bioanalyzer. Libraries were finally quantitated by qPCR, pooled in an equimolar ratio and all eight libraries run on one lane of a HiSeq1500 sequencer to obtain 50bp single end reads.

Sequencing Platform

instrument_model
Illumina HiSeq 1500

mm10

Number of total reads
16595093
Reads aligned (%)
97.8
Duplicates removed (%)
14.0
Number of peaks
304 (qval < 1E-05)

mm9

Number of total reads
16595093
Reads aligned (%)
97.5
Duplicates removed (%)
14.1
Number of peaks
345 (qval < 1E-05)

Base call quality data from DBCLS SRA