Antigen

Antigen Class

Histone

Antigen

H3K4me3

Cell type

Cell type Class

Placenta

Cell type

Placenta

MeSH Description

A highly vascularized mammalian fetal-maternal organ and major site of transport of oxygen, nutrients, and fetal waste products. It includes a fetal portion (CHORIONIC VILLI) derived from TROPHOBLASTS and a maternal portion (DECIDUA) derived from the uterine ENDOMETRIUM. The placenta produces an array of steroid, protein and peptide hormones (PLACENTAL HORMONES).

Sample

source_name

Placenta

tissue

Placenta

strain

FVB/NJxCAST/EiJ

age

E12.5

chip antibody

H3K4me3 (Millipore, 07-473, lot 2384705)

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

38317593

Reads aligned (%)

90.8

Duplicates removed (%)

24.6

Number of peaks

24258 (qval < 1E-05)

mm9

Number of total reads

38317593

Reads aligned (%)

90.4

Duplicates removed (%)

24.4

Number of peaks

24168 (qval < 1E-05)