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RNA-seq of staged embryos

ABSTRACT: RNA-seq of staged embryos

PROVIDER: PRJNA678811 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13070849_1.fastq.gz	Fastqsanger.gz
	SRR13070849_2.fastq.gz	Fastqsanger.gz
	SRR13070850_1.fastq.gz	Fastqsanger.gz
	SRR13070850_2.fastq.gz	Fastqsanger.gz
	SRR13070851_1.fastq.gz	Fastqsanger.gz

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Project description:RNA from seven adult mouse tissues, four staged whole mouse embryos, ES cells, 3 day and 28 day embryoid bodies was profiled against the microRNA microarray. A custom microarray platform for analysis of microRNA gene expression; Nature Methods 1, 47 - 53 (2004) Keywords = microRNA Keywords = miRNA Keywords: other

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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. Notes about samples and libraries: (1) A combination of litter identifier and embryo identifier within a litter will unambiguously identify a single embryo used in this study. (2) There is a margin of error for the somite-stage information (+/- 1 somite) because some embryos could be in between somite stages. (3) Sex of the embryos was determined post-RNA-seq by looking at the expression of Xist (strong expression in females only). (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 ).

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Expression data of wild-type and dcl1-15 torpedo-staged embryos

Project description:Severe loss-of-function alleles of DCL1 are embryonic lethal. Defects in cell division were seen as early as the globular stage in the strong loss-of-function allele dcl1-15. Phenotypic work with dcl1-15 and the null allele dcl1-5 suggested that, in addition to the severe patterning defects, the mutants were maturing earlier than wild-type embryos. We performed global gene expression analysis of dcl1-15 and wild-type torpedo staged embryos to examine this maturation phenotype further. The results suggested that DCL1 is a heterochronic gene. Comparisons to a time series of embryo development (http://www.seedgenenetwork.net/arabidopsis) showed that the genes differentially expressed in dcl1-15 embryos behaved more like green-cotyledon stage embryos than torpedo embryos.

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RNA-seq of staged embryos

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