Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Strand-specific RNA-seq of somite-staged pure-bred wild-type mouse embryos from the Mouse Genetics Project/ DMDD

ABSTRACT: 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 ).

ORGANISM(S): Mus musculus

SUBMITTER: John Collins

PROVIDER: E-ERAD-499 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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. 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) All knockouts in the parents or grandparents are for embryonic lethal genes. (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. (5) Sex of the embryos was determined post-RNA-seq by looking at the expression of Xist (strong expression in females only). (6) Library constructon batch refers to batch of sample handling post RNA-extraction (size selection, PCR amplification during library preparataion). (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. 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/ .

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. Total RNA was extracted from somite number staged homozygous mutant, heterozygous and sibling wild-type E9.5 whole C57BL/6N embryos and DNase treated. The embryos were derived from Mouse Genetics Programme gene knockout lines defined as homozygous embryonic lethal (http://www.sanger.ac.uk/science/collaboration/mouse-resource-portal). Stranded RNA-seq libraries were constructed using the Illumina TruSeq Stranded RNA protocol with oligo dT pulldown. Notes about samples and libraries: (1) The knockout alleles in this project were: Cnot4: Cnot4^tm1b(EUCOMM)Wtsi ; Ssr2: Ssr2^tm1b(EUCOMM)Wtsi ; 4933434E20Rik: 4933434E20Rik^tm1a(EUCOMM)Wtsi ; 1700007K13Rik: 1700007K13Rik^tm2b(EUCOMM)Wtsi ; Camsap3: Camsap3^tm1a(EUCOMM)Wtsi ; Anks6: Anks6^tm1b(KOMP)Wtsi ; Pdzk1: Pdzk1^tm2b(EUCOMM)Wtsi ; Otud7b: Otud7b^tm1b(EUCOMM)Wtsi ; Adamts3: Adamts3^tm1b(KOMP)Wtsi; Mir96: Mir96^tm2.2WTSI ; Cyp11a1: Cyp11a1^tm1b(EUCOMM)Hmgu and Traf6: Traf6^tm2a(EUCOMM)Wtsi. (2) A combination of litter identifier and embryo identifier within a litter will unambiguously identify a single embryo used in this study. (3) There is a margin of error for the somite-stage information (+/- 1 somite) because some embryos could be in between somite stages. (4) There are a minimum of three biological replicates per line. (5) Sex of the embryos was determined post-RNA-seq by looking at the expression of Xist (strong expression in females only). (6) Libraries were constructed in batches comprising multiple litters from one line from RNA-extraction to sequencing. 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/ .

Dataset Information

Strand-specific RNA-seq of somite-staged pure-bred wild-type mouse embryos from the Mouse Genetics Project/ DMDD

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