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ABSTRACT: Mediterranean Sponges metagenomes

PROVIDER: PRJNA683751 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13222438_1.fastq.gz	Fastqsanger.gz
	SRR13222438_2.fastq.gz	Fastqsanger.gz
	SRR13222439_1.fastq.gz	Fastqsanger.gz
	SRR13222439_2.fastq.gz	Fastqsanger.gz
	SRR13222440_1.fastq.gz	Fastqsanger.gz

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Transcriptomic profiles of two sponge species upon exposure to microbial-associated molecular patterns (lipopolysaccharide and peptidoglycan) compared against control (sterile artificial seawater)

Project description:The interaction of animals with microbes relies on the specific recognition of microbial-derived molecules by receptors of the immune system. Sponges (phylum Porifera), as sister group of the Eumetazoa, provide insights into conserved mechanisms for animal-microbe crosstalk, but empirical data is limited. Here we aimed to characterize the immune response of sponges upon microbial stimuli by RNA-Seq. Two sponges species from the Mediterranean Sea, Aplysina aerophoba and Dysidea avara, were challenged with microbial-associated molecular patterns (lipopolysaccharide and peptidoglycan) or sterile artificial seawater (control) in aquarium experiments. Sponge tissue samples were collected 1h, 3h, and 5h after treatment. The response of the sponges to the treatments was assessed by differential gene expression analysis of RNA-Seq data. For each species, we compared the transcriptomic profiles of the samples in MAMP treatment to control within each time point.

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Screening and validation of lncRNAs and circRNAs as miRNA sponges [siRNA, miRNA-2_0]

Project description:Intensive research in past two decades has uncovered the presence and importance of noncoding RNAs (ncRNAs), which includes microRNAs (miRs) and long ncRNAs (lncRNAs). These two classes of ncRNAs interact to a certain extent, as some lncRNAs bind to miRs to sequester them. Such lncRNAs are collectively called 'competing endogenous RNAs' or 'miRNA sponges'. In this study, we screened for lncRNAs that may act as miRNA sponges using the publicly available data sets and databases. To uncover the roles of miRNA sponges, loss-of-function experiments were conducted, which revealed the biological roles as miRNA sponges. LINC00324 is important for the cell survival by binding to miR-615-5p leading to the de-repression of its target BTG2 LOC400043 controls several biological functions via sequestering miR-28-3p and miR-96-5p, thereby changing the expressions of transcriptional regulators. Finally, we also screened for circular RNAs (circRNAs) that may function as miRNA sponges. The results were negative at least for the selected circRNAs in this study. In conclusion, miRNA sponges can be identified by applying a series of bioinformatics techniques and validated with biological experiments.

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