Transcriptomic profiling of somite staged second generation genotypically wildtype embryos of mixed G0 lineage from the Mouse Genetics Project DMDD

ABSTRACT: 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/ .

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER: John Collins 

PROVIDER: E-ERAD-401 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress