Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Embryo
Cell type
Yolk Sac
MeSH Description
The first of four extra-embryonic membranes to form during EMBRYOGENESIS. In REPTILES and BIRDS, it arises from endoderm and mesoderm to incorporate the EGG YOLK into the DIGESTIVE TRACT for nourishing the embryo. In placental MAMMALS, its nutritional function is vestigial; however, it is the source of INTESTINAL MUCOSA; BLOOD CELLS; and GERM CELLS. It is sometimes called the vitelline sac, which should not be confused with the VITELLINE MEMBRANE of the egg.

Attributes by original data submitter

Sample

source_name
Visceral yolk sac endoderm
tissue
Visceral yolk sac endoderm
strain
FVB/NJxCAST/EiJ
age
E12.5
chip antibody
H3K4me3 (Millipore, 07-473, lot 2019729)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Total RNA and DNA were extracted using TRI-reagent (Sigma-Aldrich T9424) according to the manufacturers protocol. Total RNA was DNaseI treated using the DNA-FreeTM kit (Ambion). RNA-seq: 3ug Ribosomal RNA was depleted from total DNaseI-treated RNA using the RiboZero rRNA removal kit (Human/Mouse/Rat) (Epicentre). Strand-specific RNA-seq libraries were prepared employing the TruSeq RNA Sample Prep Kit v2 (Illumina) modified as described in Sultan et al. 2012 for strand-specific sequencing. ChIP-seq: Native ChIP was conducted as described in Regha et al. 2007. ChIP-seq libraries were prepared using the TruSeq ChIP Sample Prep Kit (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
58183995
Reads aligned (%)
87.8
Duplicates removed (%)
37.9
Number of peaks
29486 (qval < 1E-05)

mm9

Number of total reads
58183995
Reads aligned (%)
87.6
Duplicates removed (%)
37.9
Number of peaks
29655 (qval < 1E-05)

Base call quality data from DBCLS SRA