# _embedded.samples[].characteristics.sample characteristics[].text
Purified B cells from healthy human donor

# _embedded.samples[].characteristics.sample characteristics[].text
Purified B cells from healthy human donor

# _embedded.samples[].characteristics.description[].text
d-CPCTRY_D3, Analysis conducted at Duke University

# _embedded.samples[].characteristics.submission description[].text
Animal and plant genomes produce numerous small RNAs (smRNAs) regulating gene expression affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous microRNAs and potential gene targets, we conducted smRNA and mRNA expression profiling over nine experimental treatments of cultures from the dinoflagellate Symbiodinium sp. A1, a photosynthetic symbiont of scleractinian corals. We identified a total of 75 novel smRNAs in Symbiodinum sp. A1 that share stringent key features with functional microRNAs from other model organisms. A subset of 38 smRNAs was predicted independently over all nine treatments and their putative gene targets were identified. We found 3,187 animal-like target sites in the 3'UTRs of 12,858 mRNAs and 53 plant-like target sites in 51,917 genes. We assembled a transcriptome of 58,649 genes and determined differentially expressed genes (DEGs) between treatments. Heat stress was found to produce a much larger number of DEGs than other treatments. Analysis of DEGs also revealed that minicircle-encoded photosynthesis proteins seem to be common targets of transcriptional regulation. Furthermore, we identified the core RNAi protein machinery in Symbiodinium. Integration of smRNA and mRNA expression profiling identified a variety of processes that could be under microRNA control, e.g. regulation of translation, DNA modification, and chromatin silencing. Given that Symbiodinium seems to have a paucity of transcription factors and differentially expressed genes, identification and characterization of its smRNA repertoire establishes the possibility of a range of gene regulatory mechanisms in dinoflagellates acting post-transcriptionally. Symbiodinium cultures were treated with nine different conditions: cold shock, cold stress, heat stress, heat shock, hyposalinity, hypersalinity, dark stress, dark cycle and control.

# _embedded.samples[].characteristics.submission title[].text
Integrating microRNA and mRNA expression profiling in Symbiodinium, the dinoflagellate symbiont of reef-building corals (smRNA)

# _embedded.samples[].organization[].Name
King Abdullah University of Science and Technology

# _embedded.samples[].organization[].Name
King Abdullah University of Science and Technology

# _embedded.samples[].characteristics.description[].text
Fragment from colony 2 taken from control aquarium at time zero.

# _embedded.samples[].characteristics.description[].text
Gene expression analysis of pollen-pistil interactions in Arabidopsis

# _embedded.samples[].characteristics.sample source name[].text
Arabidopsis pistils 3.5 hours after pollination

# _embedded.samples[].characteristics.description[].text
RMA expression value derived from Affymetrix power tools software; core-gene analysis

# _embedded.samples[].organization[].Name
Université Paris Descartes - Hopital Necker-Enfants Malades

# _embedded.samples[].organization[].Name
Flanders Institute for Biotechnology (VIB)

# _embedded.samples[].characteristics.description[].text
m-CSLD3_64, Analysis conducted at the University of Michigan

# _embedded.samples[].organization[].Name
Flanders Institute for Biotechnology (VIB)

# _embedded.samples[].characteristics.description[].text
RMA expression value derived from Affymetrix power tools software; core-gene analysis

# _embedded.samples[].organization[].Name
Université Paris Descartes - Hopital Necker-Enfants Malades

# _embedded.samples[].characteristics.description[].text
Fragment from colony 4 taken from experimental (dark treated) aquarium after nine days.

# _embedded.samples[].characteristics.sample characteristics[].text
Purified B cells from healthy human donor