Transcription profiling by RNA-Seq mouse embryos
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REPOSITORIES: ENA
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Project description:Mutations in the transcription factor p63 underlie of a series of human malformation syndromes which are defined by a combination of epidermal, limb and craniofacial abnormalities including cleft lip and palate. Transcription profiling was performed to determine the role of p63 in vivo mouse palatal shelves. RNA-seq analysis was done of palatal shelves dissected from E10.5, E11.5, E12.5, E13.5 and E14.5 mouse embryos.
2017-06-12 | E-MTAB-3157 | biostudies-arrayexpress
Project description:Zygotic transcription of ZGA staged embryos [GRO-seq]
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Project description:Transcription profiling by RNA-seq
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Project description:Fertilization triggers a transcription program mouse & human one-cell embryos
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Project description:Transcription profiling of mouse development The experiment were perfomed as a part of our Vertebrate Evo-Devo project. The aim of the project is to compare transcription profiles of normal (unmanipulated, wild-type, whole embryo) vertebrate embryos.
2011-04-05 | GSE28389 | GEO
Project description:DNase-seq profile of E11.5 whole mouse embryos
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Project description:An increasing number of studies, including mutant expression profiling and comparative transcriptomic analyses, require reference RNA-seq data collections in mice. Particularly, to complement previous profiling data sets based on arrays, a full RNA-seq developmental series will be required for whole embryos. E10.5 is a key reference stage as it represents the early organogenesis stage. Here, we have performed high-throughput sequencing of total RNA form whole mice embryos at embryonic stage E10.5. Sequencing of the total RNA of whole embryos of mouse at embryonic stage E10.5.
2014-03-25 | E-GEOD-47033 | biostudies-arrayexpress
Project description:<p>RNA sequencing was performed on human DRGs and relative gene abundances were calculated.</p> <p>Various analyses were performed:</p> <p> <ol> <li>Human DRG gene expression profiles were contrasted with a panel of gene expression profiles of relevant tissues in human and mouse ( integrating, among other sources, datasets from ENCODE and GTex ) in order to identify.</li> <ol type="a"> <li>DRG-enriched gene expression, co-expression modules of DRG-expressed genes, and key transcriptional regulators in humans.</li> <li>Contrasting the human and mouse DRG transcriptomes to identify DRG-enriched gene expression patterns that were conserved between human and mouse, identifying putative cell types of expression of these genes, and potential known drugs that might target the corresponding gene products.</li> <li>Characterization of non-coding RNA profile of human and mouse DRGs.</li> <li>Characterization of DRG-enriched alternative splicing and alternative transcription start site usage based transcript variants in humans and mouse, and the overlap between these two species.</li> <li>Contrasting of human DRG and GTex human tibial nerve samples to identify putative axonally transported mRNAs in sensory neurons.</li> </ol> <li>Human DRG transcriptomes from donors suffering from neuropathic and/or chronic pain were contrasted with controls to identify.</li> <ol type="a"> <li>Differentially expressed genes, pathways and regulators path play a potential role in neuronal plasticity, electrophysiological activity, immune signaling and response.</li> <li>Predictive models (Random Forests) were built to jointly predict the sex and pain state of samples based on information contained solely in autosomal gene expression profile.</li> <li>Gene co-expression modules were identified and gene set enrichment analysis performed.to identify sample - pathway associations, and to broadly characterize plasticity in human DRG cell types.</li> </ol> </ol> </p>
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Project description:Following fertilization, the new embryo reprograms parental genomes to begin transcription (embryonic genome activation, EGA). EGA is indispensable for development, but its dynamics, profile or when it initiates in vertebrates are unknown. We here characterize the onset of transcription in mouse one-cell embryos. Precise embryo staging eliminated noise to reveal a cascading program of de novo transcription initiating within six hours of fertilization. This immediate EGA (iEGA) utilized canonical promoters, produced spliced transcripts, was distinctive and predominantly driven by the maternal genome. Expression represented pathways not only associated with embryo development but with cancer. In human one-cell embryos, hundreds of genes were up-regulated, days earlier than thought, with conservation to mouse iEGA. These findings provide a functional basis for epigenetic analysis in early-stage embryos and illuminate networks governing totipotency and other cell-fate transitions.
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