Open Access Highly Accessed Research article

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

Sebastian Baumgarten1, Till Bayer1, Manuel Aranda1, Yi Jin Liew12, Adrian Carr2, Gos Micklem2 and Christian R Voolstra1*

Author Affiliations

1 Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955, Saudi Arabia

2 Cambridge Systems Biology Centre & Department of Genetics, University of Cambridge, Cambridge, UK

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BMC Genomics 2013, 14:704  doi:10.1186/1471-2164-14-704

Published: 12 October 2013

Additional files

Additional file 1::

miRDeep2 output of the 21 identified smRNAs.

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Open Data

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).

Format: XLSX Size: 228KB Download file

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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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Open Data

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).

Format: XLSX Size: 440KB Download file

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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).

Format: XLSX Size: 70KB Download file

Open Data

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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Open Data

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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Open Data

Additional file 11:

Table detailing enrichment of GO terms of negatively and positively correlated smRNA-mRNA expression pairs.

Format: XLSX Size: 35KB Download file

Open Data