GSE160455
Total RNA sequencing analysis to measure the effect of Ehmt2 (G9a, Bat8) deficiencies in the placentas of somite-satge matched embryos
The experiment was designed to test the role of EHMT2 in developmental regulation of transcription and imprinted gene regulation. We collected samples that allow us to interpret transcription changes due to different genetically induced deficiencies in the Ehmt2 gene encoding the H3K9 methyltransferase EHMT2. The deficiencies included zygotic homozygosity, maternal mutation, and parental (maternal, paternal, and biparental) haploinsufficiencies, and their respective controls. The time of collection was between 8.5 and 9.5 dpc to allow collecting placentas from somite-stage matched embryos and detect transcriptome changes shortly before the death of homozygous mutant embryos at 10.5 dpc. Overall design: We performed allele-specific and RNA strain-specific RNA-seq analysis of total RNA samples isolated from individual, 8.5-9.5 dpc placentas of somite stage-matched embryos carrying different deficiencies of Ehmt2. The genotypes and parental genotypes regarding the Ehmt2 mutant allele varied to allow detecting robust or subtle RNA changes due to the specific deficiencies in EHMT2 function. Maternal mutant, maternal haploinsufficient, paternal haploinsufficient and control placentas were collected at the 6-somite stage. Zygotic homozygous and wild type placentas were collected at the 6-somite and 12-somite stage to allow measuring transcriptomic differences in the progression of development. Reciprocal mouse crosses between the 129S1 and JF1/Ms mouse strains were used to generate the placentas to allow distingushing the parental alleles. Four replicate samples (2 males and 2 females) were collected for RNAseq analysis from each condition above. Total RNA was deep sequenced to allow detecting non-coding RNAs.