PREDICT
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Homo sapiens
SUBMITTER:
PROVIDER: E-ERAD-16 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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: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>
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