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

Thumbnail
Name:
Article - BMC Genomics - Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals - 2013.pdf
Size:
1.037Mb
Format:
PDF
Description:
Article - Full Text
Download
Thumbnail
Name:
Additional File 1 - miRDeep2 output of the 21 identified smRNAs.pdf
Size:
287.2Kb
Format:
PDF
Description:
Additional File 1 - miRDeep2 output of the 21 identified smRNAs
Download
Thumbnail
Name:
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
Size:
227.8Kb
Format:
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)
Download
Thumbnail
Name:
Additional File 3 - Table detailing the annotated plant-like targets assorted by seed matching.xlsx
Size:
17.22Kb
Format:
Microsoft Excel 2007
Description:
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).
Download
Thumbnail
Name:
Additional File 4 - Annotation of genes from the Symbiodinium microadriaticum transcriptome assembly.xlsx
Size:
3.931Mb
Format:
Microsoft Excel 2007
Description:
Additional File 4 - Annotation of genes from the Symbiodinium microadriaticum transcriptome assembly
Download
Thumbnail
Name:
Additional File 5 - FPKM expression estimates for 58,649 genes assorted by experimental treatment.xlsx
Size:
6.369Mb
Format:
Microsoft Excel 2007
Description:
Additional File 5 - FPKM expression estimates for 58,649 genes assorted by experimental treatment
Download
Thumbnail
Name:
Additional File 6 - Details the differentially expressed genes (DEGs) assorted by fold change and experimental treatment.xlsx
Size:
439.5Kb
Format:
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).
Download
Thumbnail
Name:
Additional File 7 - Table detailing enriched GO terms within the differentially expressed genes assorted by experimental treatment.xlsx
Size:
69.98Kb
Format:
Microsoft Excel 2007
Description:
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).
Download
Thumbnail
Name:
Additional File 8 - Alignment of functional domains of the Symbiodinium microadriaticum homolog.pdf
Size:
1.106Mb
Format:
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.
Download
Thumbnail
Name:
Additional File 9 - Alignment of functional domains of the Symbiodinium microadriaticum homolog.pdf
Size:
3.439Mb
Format:
PDF
Description:
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.
Download
Thumbnail
Name:
Additional File 10 - Alignment of functional domains of the Symbiodinium microadriaticum homolog of the small RNA.pdf
Size:
847.5Kb
Format:
PDF
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.
Download
Thumbnail
Name:
Additional File 11 - Table detailing enrichment of GO terms of negatively and positively correlated smRNA-mRNA expression pairs.xlsx
Size:
35.32Kb
Format:
Microsoft Excel 2007
Description:
Additional File 11 - Table detailing enrichment of GO terms of negatively and positively correlated smRNA-mRNA expression pairs
Download
View more files
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/
Collections
Articles; Biological and Environmental Sciences and Engineering (BESE) Division; Red Sea Research Center (RSRC); Marine Science Program; Reef Genomics, part of the Global Ocean Genome Project