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Seawater and Freshwater microbiome

ABSTRACT: Seawater and Freshwater microbiome Targeted loci environmental

PROVIDER: PRJNA662461 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12631646.fastq.gz	Fastqsanger.gz
	SRR12631647.fastq.gz	Fastqsanger.gz
	SRR12631648.fastq.gz	Fastqsanger.gz
	SRR12631649.fastq.gz	Fastqsanger.gz
	SRR12631650.fastq.gz	Fastqsanger.gz

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Transcriptomic analysis of trout gill ionocytes in freshwater and seawater using laser capture microdissection combined with microarray analysis

Project description:Fish gills represent a complex organ that perform multiple physiological functions and is composed of several cell types. Among these cells, ionocytes are implicated in the maintenance of ion homeostasis. However, because the ionocyte represents only a small percent of whole gill tissue, its specific transcriptome can be overlooked among the numerous cell types included in the gill. The objective of this study is to better understand ionocyte functions by comparing the RNA expression of this cell type in freshwater and seawater adapted rainbow trout. To realize this objective, ionocytes were captured from gill cryosections using laser capture microdissection after immunohistochemistry. Then, transcriptome analyses were performed on an Agilent trout oligonucleotide microarray. Gene expression analysis identified 108 unique annotated genes differentially expressed between freshwater and seawater ionocytes, with a gene fold higher than 3. Most of these genes were up regulated in freshwater cells. Interestingly, several genes implicated in ion transport, extracellular matrix and structural cellular proteins appeared up regulated in freshwater ionocytes. Among them, several ion transporters, such as CIC2, SLC26A6, and NBC, were validated by qPCR and/or in situ hybridization. The latter technique allowed us to localize the transcripts of these ion transporters in only ionocytes and more particularly in the freshwater cells. Genes involved in metabolism and also several genes implicated in transcriptional regulation, cell signaling and the cell cycle were also over-expressed in freshwater ionocytes. In conclusion, laser capture microdissection combined with microarray analysis allowed for the determination of the cell signature of scarce cells in fish gills, such as ionocytes, and aided characterization of the transcriptome of these cells in freshwater and seawater adapted trout.

2015-10-08 | GSE69409 | GEO

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Project description:seawater metagenome Targeted loci environmental