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Series GSE156538 Query DataSets for GSE156538
Status Public on Nov 01, 2021
Title Whole genome RNA sequencing analysis to measure the effect of Ehmt2 (G9a, Bat8) deficiencies in somite-staged mouse embryos
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The experiment was designed to interpret transcription changes in embryos that are developmentally delayed 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 age of the embryos was between 8.5 and 9.5 dpc to allow collecting somite-stage matched embryos and detect transcriptome changes shortly before the death of homozygous mutant embryos at 10.5 dpc. Analyzing the homozygous mutants in a novel four-way comparison we distinguished differentially expressed genes (DEGs) that are direct effects of the mutation from those that correspond to embryo development. We separated the developmental DEGs that occur regardless of EHMT2 between the 6-and 12-somite stages, and then identified those developmental DEGs that uniquely change in either the normal or the mutant development. Ehmt2 zygotic and maternal mutant embryos display an increased variance, suggesting that EHMT2 is responsible for narrowing the transcriptional noise after gastrulation. Some transposable element classes correlate with genotype, but others correlate with developmental stage. EHMT2 is required for suppressing long noncoding transcripts that initiate in transposable elements predominantly of the ERVK-class. The ERVK promoters of noncanonical imprinted genes in the embryo require EHMT2 for biallelic silencing and DNA methylation. The transcriptome of delayed parental haploinsufficient wild type embryos is normal, consistent with their good survival prospects. Our four-way comparison approach is generally applicable to functional dissection of essential transcriptional regulators during development.
 
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 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 embryos were collected at the 6-somite stage. Zygotic homozygous and wild type embryos 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 embryos to allow distingushing the parental alleles. Four replicate embryos (2 males and 2 females) were collected for RNAseq analysis from each condition above. Additionally, two of the rarely found maternal-zygotic mutant female embryos were included. Total RNA was deep sequenced to allow detecting non-coding RNAs.
 
Contributor(s) Tie-Bo Z, Nicholas PG, Piroska SE
Citation(s) 34793451
Submission date Aug 20, 2020
Last update date Dec 01, 2021
Contact name Piroska E Szabó
E-mail(s) piroska.szabo@vai.org
Organization name Van Andel Institute
Department Epigenetics
Lab Developmental Reprogramming
Street address 333 Bostwick ave NE
City Grand Rapids
State/province MI
ZIP/Postal code 49503
Country USA
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (50)
GSM4733187 Control 6-somite embryo (1xJ cross) #1
GSM4733188 Control 6-somite embryo (1xJ cross) #2
GSM4733189 Control 6-somite embryo (1xJ cross) #3
Relations
BioProject PRJNA658312
SRA SRP278197

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE156538_Embryo_AlleleCounts.txt.gz 5.8 Mb (ftp)(http) TXT
GSE156538_GeneCounts_mm10_Embryo.txt.gz 5.4 Mb (ftp)(http) TXT
GSE156538_RAW.tar 7.0 Gb (http)(custom) TAR (of BW)
GSE156538_RepeatCounts_mm10_Embryo.txt.gz 92.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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