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Title: Transcriptome conservation of the D. discoideum and D. purpureum developmental programs revealed through RNA-sequencing      
availability:
available
aggregation:
instance of dataset
privacy:
not applicable
refinement:
curated
dateReleased:
11-06-2012
ID:
E-GEOD-17637
description:
Cross species comparison of genomes and transcriptomes is a powerful tool for understanding underlying biological processes, accurate functional classification of genes, and discovery of novel elements. The shift to next-generation sequencing platforms has tremendously accelerated the analysis of genomes and transcriptomes. The use of this technology for transcriptome analysis has many advantages over hybridization based technologies, including higher sensitivity and specificity, and eliminates the need for probe design. Using Illumina sequencing of mRNAs, we have captured the global transcriptional profiles of the developmental cycles of D. discoideum and D. purpureum. The morphology and transcriptional profiles in these two species have been largely conserved even after greater than 300 million years of divergence. We also captured the transcriptional profiles of prespore and prestalk cells from both species. The RNA-seq results correlate well with previously known markers and reveal many new transcripts with unique developmental regulation and cell type enrichment. Our analysis provides the first complete picture of the transcriptional landscape in both D. discoideum and D. purpureum. Transcriptional abundance of over 13,900 genome elements from seven time points of development, and prespore/prestalk cell types will be available through a graphical, highly-interactive, explorative web interface at: http://www.ailab.si/dictyexpress , which currently displays all of our published microarray data. Sequence coverage at a single nucleotide resolution will also be available through an interactive genome browser. These data, from morphology to genome to transcriptome, provide a global picture of the developmental cycles of D. discoideum and D. purpureum and will facilitate the functional classification of genes, as well as discovery of novel genes, splice variants, regulatory elements and non-coding RNAs. Keywords: Transcriptome Analysis Examination of 7 developmental time points in two cell types with 2 biological replicates for each sample.
keywords:
RNA-seq of coding RNA
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HTML
storedIn:
Array Express
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primary:
true
accessURL: https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-17637
format:
JSON
storedIn:
OmicsDI
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accessType:
download
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none
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none
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false
accessURL: www.omicsdi.org/ws/dataset/arrayexpress-repository/E-GEOD-17637.json
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XML
storedIn:
OmicsDI
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not compressed
accessType:
download
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none
authentication:
none
primary:
false
accessURL: http://www.omicsdi.org/ws/dataset/arrayexpress-repository/E-GEOD-17637.xml
ID:
SCR:014747
name:
Omics Discovery Index
abbreviation:
OmicsDI
homePage: http://www.omicsdi.org/