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

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    Article - BMC Genomics - Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals - 2013.pdf
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    Article - Full Text
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    Additional File 1 - miRDeep2 output of the 21 identified smRNAs.pdf
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    287.2Kb
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    Additional File 1 - miRDeep2 output of the 21 identified smRNAs
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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).xlsx
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    227.8Kb
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    Microsoft Excel 2007
    Description:
    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 - Table detailing the annotated plant-like targets assorted by seed matching.xlsx
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    17.22Kb
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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.xlsx
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    3.931Mb
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    Microsoft Excel 2007
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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.xlsx
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    6.369Mb
    Format:
    Microsoft Excel 2007
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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.xlsx
    Size:
    439.5Kb
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    Microsoft Excel 2007
    Description:
    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 - Table detailing enriched GO terms within the differentially expressed genes assorted by experimental treatment.xlsx
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    69.98Kb
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    Microsoft Excel 2007
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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 - Alignment of functional domains of the Symbiodinium microadriaticum homolog.pdf
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    1.106Mb
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    PDF
    Description:
    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 the Symbiodinium microadriaticum homolog.pdf
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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 - Alignment of functional domains of the Symbiodinium microadriaticum homolog of the small RNA.pdf
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    847.5Kb
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    Description:
    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 - Table detailing enrichment of GO terms of negatively and positively correlated smRNA-mRNA expression pairs.xlsx
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    35.32Kb
    Format:
    Microsoft Excel 2007
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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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    Type
    Article
    Authors
    Baumgarten, Sebastian cc
    Bayer, Till
    Aranda, Manuel cc
    Liew, Yi Jin cc
    Carr, Adrian
    Micklem, Gos
    Voolstra, Christian R. cc
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Marine Science Program
    Red Sea Research Center (RSRC)
    Reef Genomics Lab
    Date
    2013-10-12
    Online Publication Date
    2013-10-12
    Print Publication Date
    2013
    Permanent link to this record
    http://hdl.handle.net/10754/323539
    
    Metadata
    Show full item record
    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.
    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
    Springer Nature
    Journal
    BMC Genomics
    DOI
    10.1186/1471-2164-14-704
    PubMed ID
    24119094
    PubMed Central ID
    PMC3853145
    Additional Links
    http://www.biomedcentral.com/1471-2164/14/704
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3853145/
    Relations
    Is Supplemented By:
    • [Bioproject]
      Title: Integrating microRNA and mRNA expression profiling in Symbiodinium, the dinoflagellate symbiont of reef-building coralsPublication Date: 2013-06-01. bioproject: PRJNA206215 Handle: 10754/666426
    ae974a485f413a2113503eed53cd6c53
    10.1186/1471-2164-14-704
    Scopus Count
    Collections
    Articles; Biological and Environmental Science and Engineering (BESE) Division; Red Sea Research Center (RSRC); Marine Science Program; Reef Genomics, part of the Global Ocean Genome Project

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