Antigen

Antigen Class

ATAC-Seq

Antigen

ATAC-Seq

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

e9.5_placenta

strain

CD1

developmental stage

Embryonic day 9.5

tissue

whole placenta

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

Placenta were microdissected from e9.5 timed-pregnant mice and collected in cold dPBS We performed tissue homogenization and cell lysis, following the transposition and purification steps as described previously by Buenrostro et al.( 2015). We amplified the purified DNA with adapters from the Nextera index kit (Illumina). PCR purification was performed using AMpure XP beads (Beckman Coulter) in order to remove large fragments and remaining primers. Library quality was assessed using the Bioanalyzer High Sensitivity DNA Analysis kit (Agilent) to check for proper periodicity, and the DNA concentrations were estimated using the Qubit and Bioanalyzer. Libraries were sequenced by Elim Biopharmaceuticals, Inc. using the Illumina HiSeq 2500 Rapid run platform with 50bp paired-end sequencing.

Sequencing Platform

instrument_model

Illumina HiSeq 2500

mm10

Number of total reads

36680958

Reads aligned (%)

89.1

Duplicates removed (%)

52.9

Number of peaks

4053 (qval < 1E-05)

mm9

Number of total reads

36680958

Reads aligned (%)

89.0

Duplicates removed (%)

53.0

Number of peaks

4030 (qval < 1E-05)