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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Additional File 1 - miRDeep2 output of the 21 identified smRNAs.pdf
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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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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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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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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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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
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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 - Table detailing enriched GO terms within the differentially expressed genes assorted by experimental treatment.xlsx
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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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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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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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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

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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
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