Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals.

Handle URI:
http://hdl.handle.net/10754/323539
Title:
Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals.
Authors:
Baumgarten, Sebastian ( 0000-0003-2646-7699 ) ; Bayer, Till; Aranda, Manuel ( 0000-0001-6673-016X ) ; Liew, Yi Jin; Carr, Adrian; Micklem, Gos; Voolstra, Christian R. ( 0000-0003-4555-3795 )
Abstract:
Animal and plant genomes produce numerous small RNAs (smRNAs) that regulate gene expression post-transcriptionally affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous smRNAs and potential gene targets in dinoflagellates, we conducted smRNA and mRNA expression profiling over 9 experimental treatments of cultures from Symbiodinium microadriaticum, a photosynthetic symbiont of scleractinian corals.
KAUST Department:
Red Sea Research Center (RSRC)
Citation:
Baumgarten S, Bayer T, Aranda M, Liew Y, Carr A, et al. (2013) Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals. BMC Genomics 14: 704. doi:10.1186/1471-2164-14-704.
Publisher:
BioMed Central
Journal:
BMC genomics
Issue Date:
12-Oct-2013
DOI:
10.1186/1471-2164-14-704
PubMed ID:
24119094
PubMed Central ID:
PMC3853145
Type:
Article
ISSN:
1471-2164
Additional Links:
http://www.biomedcentral.com/1471-2164/14/704; http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3853145/
Appears in Collections:
Articles; Red Sea Research Center (RSRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorBaumgarten, Sebastianen
dc.contributor.authorBayer, Tillen
dc.contributor.authorAranda, Manuelen
dc.contributor.authorLiew, Yi Jinen
dc.contributor.authorCarr, Adrianen
dc.contributor.authorMicklem, Gosen
dc.contributor.authorVoolstra, Christian R.en
dc.date.accessioned2014-07-21T13:55:13Z-
dc.date.available2014-07-21T13:55:13Z-
dc.date.issued2013-10-12en
dc.identifier.citationBaumgarten S, Bayer T, Aranda M, Liew Y, Carr A, et al. (2013) Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals. BMC Genomics 14: 704. doi:10.1186/1471-2164-14-704.en
dc.identifier.issn1471-2164en
dc.identifier.pmid24119094en
dc.identifier.doi10.1186/1471-2164-14-704en
dc.identifier.urihttp://hdl.handle.net/10754/323539en
dc.description.abstractAnimal and plant genomes produce numerous small RNAs (smRNAs) that regulate gene expression post-transcriptionally affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous smRNAs and potential gene targets in dinoflagellates, we conducted smRNA and mRNA expression profiling over 9 experimental treatments of cultures from Symbiodinium microadriaticum, a photosynthetic symbiont of scleractinian corals.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/14/704en
dc.relation.urlhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3853145/en
dc.rightsArchived with thanks to BMC genomicsen
dc.subject.meshAnimalsen
dc.subject.meshAnthozoaen
dc.subject.meshCoral Reefsen
dc.subject.meshDinoflagellidaen
dc.subject.meshGene Expression Profilingen
dc.subject.meshGene Expression Regulationen
dc.subject.meshGene Ontologyen
dc.subject.meshMicroRNAsen
dc.subject.meshPhotosynthesisen
dc.subject.meshRNA, Messengeren
dc.subject.meshSymbiosisen
dc.subject.meshTranscriptomeen
dc.subject.meshAnimalsen
dc.subject.meshAnthozoaen
dc.subject.meshCoral Reefsen
dc.subject.meshDinoflagellidaen
dc.subject.meshGene Expression Profilingen
dc.subject.meshGene Expression Regulationen
dc.subject.meshGene Ontologyen
dc.subject.meshMicroRNAsen
dc.subject.meshPhotosynthesisen
dc.subject.meshRNA, Messengeren
dc.subject.meshSymbiosisen
dc.subject.meshTranscriptomeen
dc.titleIntegrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals.en
dc.typeArticleen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.identifier.journalBMC genomicsen
dc.identifier.pmcidPMC3853145en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionCambridge Systems Biology Centre, Department of Genetics, University of Cambridge, Cambridge, United Kingdomen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorBaumgarten, Sebastianen
kaust.authorBayer, Tillen
kaust.authorAranda, Manuelen
kaust.authorLiew, Yi Jinen
kaust.authorVoolstra, Christian R.en

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  • Files 12

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      Article - BMC Genomi...
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      Article - Full Text
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      Additional File 1 - ...
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      Additional File 1 - miRDeep2 output of the 21 identified smRNAs
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      Additional File 2 - ...
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      Additional File 2 - Table detailing the annotated animal-like targets assorted by target seed properties (n = 1,720 in 3'UTRs of 12,858 mRNAs)
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      Additional File 3 - ...
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      Additional File 3 - Table detailing the annotated plant-like targets assorted by seed matching to CDS or UTR (n = 19 in 51,917 genes from the genomic gene set).
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      Additional File 4 - Annotation of genes from the Symbiodinium microadriaticum transcriptome assembly
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      Additional File 5 - FPKM expression estimates for 58,649 genes assorted by experimental treatment
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      Additional File 6 - Details the differentially expressed genes (DEGs) assorted by fold change and experimental treatment (n = 3,285 DEGs in 58,649 genes, DESeq, FDR < 0.1).
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      Additional File 7 - ...
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      Additional File 7 - Table detailing enriched GO terms within the differentially expressed genes assorted by experimental treatment (Fisher's Exact test, Alexa algorithm, P < 0.05).
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      Additional File 8 - ...
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      Additional File 8 - Alignment of functional domains of the Symbiodinium microadriaticum homolog of the endoribonuclease Dicer with homologs from model organisms (S. pombe, A. thaliana, C. elegans, D. melanogaster, H. sapiens). Key functional residues are depicted with red asterisks.
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      Additional File 9 - Alignment of functional domains of Symbiodinium microadriaticum homologs of the Argonaute effector protein with homologs from model organisms (S. pombe, A. thaliana, C. elegans, D. melanogaster, H. sapiens). Key functional residues are depicted with red asterisks.
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      Additional File 10 -...
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      Additional File 10 - Alignment of functional domains of the Symbiodinium microadriaticum homolog of the small RNA 2'-O-methyltransferase (HEN1) with homologs from model organisms (S. pombe, A. thaliana, C. elegans, D. melanogaster, H. sapiens). Key functional residues are depicted with red asterisks.
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      Additional File 11 -...
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      Additional File 11 - Table detailing enrichment of GO terms of negatively and positively correlated smRNA-mRNA expression pairs
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