Whole genome RNA sequencing analysis to measure the effect of Ehmt2 (G9a, Bat8) deficiencies in somite-staged mouse embryos
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ABSTRACT:
PROVIDER: PRJNA658312 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12482700_1.fastq.gz | Fastqsanger.gz | |||
| SRR12482700_2.fastq.gz | Fastqsanger.gz | |||
| SRR12482800_1.fastq.gz | Fastqsanger.gz | |||
| SRR12482800_2.fastq.gz | Fastqsanger.gz | |||
| SRR12482900_1.fastq.gz | Fastqsanger.gz |
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Project description: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.
2021-11-01 | GSE156538 | GEO
Project description: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.
2021-11-01 | GSE160455 | GEO
Project description:Total RNA sequencing analysis to measure the effect of Ehmt2 (G9a, Bat8) deficiencies in the placentas of somite-satge matched embryos
| PRJNA673225 | ENA
Project description:The DMDD Programme (Deciphering the Mechanisms of Developmental Disorders ) provides a free online database of morphological and molecular phenotypes from embryonic-lethal mouse gene knockouts (http://www.dmdd.org.uk/). Embryos are imaged using HREM, placentas are examined by histology and mutant embryo mRNA expression profiles are compared to wild type. To underpin these investigations we have produced a comprehensive time series of gene expression through normal embryo development. Total RNA was extracted from somite number staged wildtype embryos with no history of genetic modification in previous generations from the Mouse Genetics Programme (http://www.sanger.ac.uk/science/collaboration/mouse-resource-portal) and DNase treated. Stranded RNA-seq libraries were constructed using the Illumina TruSeq Stranded RNA protocol with oligo dT pulldown.<br> Notes about samples and libraries:<br> (1) A combination of litter identifier and embryo identifier within a litter will unambiguously identify a single embryo used in this study. </br><br> (2) There is a margin of error for the somite-stage information (+/- 1 somite) because some embryos could be in between somite stages. </br><br> (3) Sex of the embryos was determined post-RNA-seq by looking at the expression of Xist (strong expression in females only). </br><br> (4) Complementary data on genotypically wild-type mice with mixed G0 lineage and with heterozygous mutant parents can also be found in ArrayExpress under accession numbers E-ERAD-352 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-ERAD-352 ) and E-ERAD-401 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-ERAD-401 ).</br>
2016-06-01 | E-ERAD-499 | biostudies-arrayexpress
Project description:The DMDD Programme (Deciphering the Mechanisms of Developmental Disorders, https://dmdd.org.uk/) provides a free online database of morphological and molecular phenotypes from embryonic-lethal mouse gene knockouts (http://www.dmdd.org.uk/). Embryos are imaged using HREM, placentas are examined by histology and mutant embryo mRNA expression profiles are compared to wild type. To underpin these investigations we have produced a comprehensive time series of gene expression through normal embryo development. Total RNA was extracted from somite number staged, second generation genotypically wild type, C57BL/6N embryos of mixed G0 linages from the Mouse Genetics Programme (http://www.sanger.ac.uk/science/collaboration/mouse-resource-portal) and DNase treated. Stranded RNA-seq libraries were constructed using the Illumina TruSeq Stranded RNA protocol with oligo dT pulldown.<br> Notes about samples and libraries: </br><br>(1) A combination of litter identifier and embryo identifier within a litter will unambiguously identify a single embryo used in this study. </br><br>(2) There is a margin of error for the somite-stage information (+/- 1 somite) because some embryos could be in between somite stages. </br><br> (3) All knockouts in the parents or grandparents are for embryonic lethal genes. </br><br>(4) There are four biological replicates per somite-stage, with the exception of the 4-somite embryos (three biological replicates only). Altogether 111 embryos were sourced, of which 14 were sequenced twice to generate enough read depth/coverage. No new libraries were prepared for the repeated sequencing, despite the assays being assigned new ERX* accessions. </br><br> (5) Sex of the embryos was determined post-RNA-seq by looking at the expression of Xist (strong expression in females only). </br><br> (6) Library constructon batch refers to batch of sample handling post RNA-extraction (size selection, PCR amplification during library preparataion). </br><br>(7) Superbatch gathers 17 representative embryos out of the 111 embryos post RNA-extraction, and put them through the library construction pipeline as one single batch. The generated data is intended to be used for normalisation using the remove unwanted variation (RUV) method. </br> <br> This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ .</br>
2015-11-03 | E-ERAD-401 | biostudies-arrayexpress
Project description:WGBS analysis was used to map DNA methylation in response to the mutation of Ehmt2 gene at the embryonic age of 9.5 days post coitum.
2021-11-01 | GSE156539 | GEO
Project description:RNAseq from somite-matched frontonasal prominence (FNP) from E10.5 embryos at the 29-somite developmental stage
2021-05-08 | GSE174090 | GEO
Project description:RNAseq from somite-paired pre-somitic mesoderm from E8.5 embryo tailbuds at the 8-somite developmental stage
2021-05-08 | GSE174069 | GEO
Project description:The DMDD Programme (Deciphering the Mechanisms of Developmental Disorders ) provides a free online database of morphological and molecular phenotypes from embryonic-lethal mouse gene knockouts (http://www.dmdd.org.uk/). Embryos are imaged using high-resolution episcopic microscopy (HREM), placentas are examined by histology and mutant embryo mRNA expression profiles are compared to wild type. To underpin these investigations we have produced a comprehensive time series of gene expression through normal embryo development<br></br>In this study, yotal RNA was extracted from wildtype C57BL/6N sibling embryos with heterozygous parentage from the Mouse Genetics Project (http://www.dmdd.org.uk/) and DNase treated. Stranded RNAseq libraries were constructed using the Illumina TruSeq Stranded RNA protocol with oligo dT pulldown. <br></br> Notes about samples and libraries:<br></br> (1) A combination of litter identifier and embryo identifier within a litter will unambiguously identify a single embryo used in this study. <br></br> (2) There is a margin of error for the somite-stage information (+/- 1 somite) because some embryos could be in between somite stages. <br></br>(3) Sex of the embryos was determined post-RNA-seq by looking at the expression of Xist (strong expression in females only). <br></br>(4) All knockouts in the parents (and hence grandparents) are for embryonic lethal genes. <br></br> (5) There are four biological replicates per somite-stage. <br></br>(6) Complementary data on genotypically wild-type mice with mixed G0 lineage and no history of genetic modification can also be found in ArrayExpress under accession numbers E-ERAD-401 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-ERAD-401 ) and E-ERAD-499 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-ERAD-499 ) respectively.
2015-02-11 | E-ERAD-352 | biostudies-arrayexpress
Project description:We report the genome-wide occupancy of EHMT2/G9a in the RD18 embryonal rhabdomyosarcoma cell line.
2020-12-16 | GSE125960 | GEO