GSE117879
Unique Trophoblast Chromatin Environment Mediated by the PcG Protein SFMBT2 [RNA-seq]
Sfmbt2 is a paternally imprinted gene critical for the establishment and maintenance of trophoblast stem cells in mice (Miri K et al., 2013).  Inheritance of a paternal Sfmbt2 gene trap null allele (Sfmbt2gt/gt) results in embryonic lethality by e12.5 due to reduced numbers in all trophoblast cell types.  Of note, SFMBT2 is characterized as a Polycomb group (PcG) protein and is assumed to act as a master transcriptional repressor.  Through RNA-seq analysis of extraembryonic tissues acquired from both wild-type and Sfmbt2gt/gt embryos, we aim to elucidate differentially expressed genes critical for the dramatic phenotype observed in mutant embryos. Overall design: Sfmbt2gt/gt embryos were generated by intercrossing heterozygous Sfmbt2gt males and females.  Embryos were extracted at e7.5 and individually dissected into embryo and extraembryonic (i.e. ectoplacental cone and extraembryonic ectoderm) portions.  The embryonic portion was used for genotyping, and total RNA was extracted from extraembryonic portions of both wild-type (+/+) and mutant (gt/gt) embryos using Trizol.  Total RNA from pools of 12 embryos was extracted and processed by The Centre for Applied Genomics (TCAG) at The Hospital for Sick Children in Toronto.  The RNA-seq library was generated using the Illumina TruSeq protocol and was subject to paired-end next-generation sequencing on the Illumina HiSeq 2500 platform.  Two biological replicates of each were analyzed.