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ABSTRACT: Next Generation sequencing of transcriptome of Nile Crocodile (Crocodylus niloticus)

PROVIDER: PRJNA564884 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10097239_1.fastq.gz	Fastqsanger.gz
	SRR10097239_2.fastq.gz	Fastqsanger.gz
	SRR10097240_1.fastq.gz	Fastqsanger.gz
	SRR10097240_2.fastq.gz	Fastqsanger.gz
	SRR10097241.fastq.gz	Fastqsanger.gz

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Identification and characterization of microRNAs (miRNAs) and their transposable element origins in the saltwater crocodile, Crocodylus porosus

Project description:MicroRNAs (miRNAs) are 18-24 nucleotide autonomous regulatory RNA molecules found in all eukaryotes. They are involved in the regulation of a multitude of genetic and biological pathways through post transcriptional gene silencing and/or translational repression. Previous data has suggested a slow evolutionary rate for the saltwater crocodile (Crocodylus porosus) over the past several million years when compared to its closest extant relatives, the birds. Understanding genome regulation, adaptive capabilities and physiological features in the saltwater crocodile in the context of relatively slow genomic change thus holds significant potential for the investigation of genomics, evolution and adaptive studies. Utilizing eleven different tissue types and sixteen small RNA libraries, we report a catalog of 644 miRNAs in the saltwater crocodile with > 78% of miRNAs being potentially novel to crocodilians. We also predicted and identified targets for the miRNAs as well as analyzed the relationship of the miRNA repertoire to transposable elements (TEs) in the saltwater crocodile that showed an increased association of DNA transposons with miRNA biogenesis when compared to retrotransposons. Phylogenetic analysis of C. porosus miRNA expectedly revealed highest number of miRNAs in sister crocodilian clades of the American Alligator and the Indian Gharial. This work reports the first comprehensive analysis of miRNAs in Crocodylus porosus for and addresses the potential impacts of miRNAs in regulating the genome in the saltwater crocodile as well as supporting the role of TEs as a source for miRNAs, adding to the increasing evidence that TEs play a significant role in the evolution of gene regulation.

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Project description:We report RNA-Seq experiments of eye tissues from Nile rat (Arivacanthis niloticus)

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Project description:To quantify gene expression differences in olfactory epithelium between the mouse (Mus musculus) and the Nile rat (Arvicanthis niloticus), paired-end RNA sequencing (RNA-seq) was used to profile olfactory epithelium transcriptomes of six Nile rats and six mice (C57BL/6J) (one male and one female at the age of 8, 12, and 16 weeks for each species).

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Project description:Crocodylus niloticus overview

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Microarray analysis on livers of young Nile rats fed palm fruit juice

Project description:Microarray analysis on livers of young (three weeks old) Nile rats (Arvicanthis niloticus) fed with either a high carbohydrate diet only (percentage energy from carbohydrate:fat:protein = 70:10:20, 16.7 kJ/g) or a high carbohydrate diet supplemented with palm fruit juice (PFJ) (415 ml of 13000 ppm gallic acid equivalent (GAE) for a final concentration of 5.4 g GAE per kg diet or 2.7 g per 2000 kcal) PFJ (415 ml of 13000 ppm gallic acid equivalent (GAE) for a final concentration of 5.4 g GAE per kg diet or 2.7 g per 2000 kcal) was supplemented to young Nile rats (Arvicanthis niloticus) given a high carbohydrate diet (percentage energy from carbohydrate:fat:protein = 70:10:20, 16.7 kJ/g) to observe for possible anti-diabetic effects. Livers were harvested four weeks after the feeding regimen for gene expression studies. Results from the microarray data analysis carried out show that rats given PFJ had down-regulated insulin signalling, consistent with anti-diabetic effects observed in vivo. Total RNA obtained from livers of young Nile rats (Arvicanthis niloticus) given PFJ in a high carbohydrate diet (four weeks after the feeding regimen) were compared to controls (three replicates in the treatment group versus four replicates in the control group)

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