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E-MTAB-5224

ABSTRACT: Strand-specific RNA-seq of somite-staged whole embryos from gene knockout lines comparing homozygous mutant against wild-type from the Mouse Genetics Project/DMDD

PROVIDER: E-MTAB-5224 | ExpressionAtlas | 2019-05-14

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-MTAB-5224-analysis-methods.tsv	Tabular
	E-MTAB-5224-analytics.tsv	Tabular
	E-MTAB-5224-analytics.tsv.bak	Tabular
	E-MTAB-5224-analytics.with-g2_g1.tsv	Tabular
	E-MTAB-5224-analytics.without-g2_g1.tsv	Tabular

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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. 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/ .

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E-MTAB-5224

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