Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1033547 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26561700_1.fastq.gz | Fastqsanger.gz | |||
| SRR26561700_2.fastq.gz | Fastqsanger.gz | |||
| SRR26561701_1.fastq.gz | Fastqsanger.gz | |||
| SRR26561701_2.fastq.gz | Fastqsanger.gz | |||
| SRR26561702_1.fastq.gz | Fastqsanger.gz |
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Project description:Amphibian populations around the world are threatened by an emerging infectious pathogen, the chytrid fungus Batrachochytrium dendrobatidis (Bd). How can a fungal skin infection kill such a broad range of amphibian hosts? And why are certain species particularly susceptible to the impacts of Bd? Here we use a genomics approach to understand the genetic response of multiple susceptible frog species to Bd infection. We characterize the transcriptomes of two closely-related endangered frog species (Rana muscosa and Rana sierrae) and analyze whole genome expression profiles from frogs in controlled Bd-infection experiments. We integrate the Rana results with a comparable dataset from a more distantly-related susceptible species (Silurana tropicalis). We demonstrate that Bd-infected frogs show massive disruption of skin function and show no evidence of a robust immune response. The genetic response to infection is shared across the focal susceptible species, suggesting a common effect of Bd on susceptible frogs. A total of five (12-plex) chips were analyzed from 60 samples comprising 2 conditions (control and infected), 3 tissues (skin, liver and spleen) and 2 timepoints (early and late). Three biological replicates were used for each condition and tissue at each time point. Twentyfour arrays were analyzed for skin samples, 24 for liver, and 12 for spleen. The same dye, Cy5, was used for all samples.
2012-04-30 | E-GEOD-34235 | biostudies-arrayexpress
Project description:Amphibian populations around the world are threatened by an emerging infectious pathogen, the chytrid fungus Batrachochytrium dendrobatidis (Bd). How can a fungal skin infection kill such a broad range of amphibian hosts? And why are certain species particularly susceptible to the impacts of Bd? Here we use a genomics approach to understand the genetic response of multiple susceptible frog species to Bd infection. We characterize the transcriptomes of two closely-related endangered frog species (Rana muscosa and Rana sierrae) and analyze whole genome expression profiles from frogs in controlled Bd-infection experiments. We integrate the Rana results with a comparable dataset from a more distantly-related susceptible species (Silurana tropicalis). We demonstrate that Bd-infected frogs show massive disruption of skin function and show no evidence of a robust immune response. The genetic response to infection is shared across the focal susceptible species, suggesting a common effect of Bd on susceptible frogs.
2012-05-01 | GSE34235 | GEO
Project description:The fungal skin disease chytridiomycosis has caused the devastating decline and extinction of hundreds of amphibian species globally, yet the potential for evolving resistance, and the underlying pathophysiological mechanisms remain poorly understood. We exposed 406 naïve, captive-raised alpine tree frogs (Litoria verreauxii alpina) to the aetiological agent Batrachochytrium dendrobatidis in two concurrent and controlled infection experiments. We investigated (A) survival outcomes and clinical pathogen burdens between populations and clutches, and (B) individual host tissue responses to chytridiomycosis. Here we present multiple interrelated datasets associated with these exposure experiments, including animal signalment, survival and pathogen burden of 355 animals from Experiment A, and the following datasets related to 61 animals from Experiment B: animal signalment and pathogen burden; raw RNA-Seq reads from skin, liver and spleen tissues; de novo assembled transcriptomes for each tissue type; raw gene expression data; annotation data for each gene; and raw metabolite expression data from skin and liver tissues. These data provide an extensive baseline for future analyses.
2018-01-09 | MTBLS457 | MetaboLights
Project description:While nucleotide-resolution maps of genomic structural variants (SVs) have provided insights into the origin and impact on phenotypic diversity in humans, comparable maps in nonhuman primates have thus far been lacking. Using massively parallel DNA sequencing we constructed fine-resolution, species-specific structural variation and segmental duplication maps for five chimpanzees, five orang-utans, and five rhesus macaques. The SV maps, comprising thousands of deletions, duplications, and mobile element insertions, revealed a high activity of retrotransposition in macaques. Non-allelic homologous recombination, linked with genomic architecture, primarily shaped the genomes of great apes resulting in different SV formation mechanism landscapes across species, with distinct functional consequences. Transcriptome analyses across nonhuman primates and humans revealed significant effects of species-specific gene duplications on gene expression, with these effects displaying remarkable diversity in direction and magnitude. Thirteen inter-species gene duplications coincided with the species-specific gain of expression in a new tissue, implicating these duplications in function acquisition.
2013-08-10 | GSE45741 | GEO
Project description:Dogs have become a valuable model in exploring multifaceted diseases and biology relevant to human health. Despite large-scale dog genome projects producing high-quality draft references, a comprehensive annotation of functional elements is still lacking. We addressed this through integrative next-generation sequencing of transcriptomes paired with five histone marks and DNA methylome profiling across 11 tissue types, deciphering the dog’s epigenetic code by defining distinct chromatin states, super-enhancer and methylome landscapes, and thus showed that these regions are associated with a wide range of biological functions and cell/tissue identity. In addition, we confirmed that the phenotype-associated variants are enriched in tissue-specific regulatory regions and, therefore, the tissue of origin of the variants can be traced. Ultimately, we delineated conserved and dynamic epigenomic changes at the tissue- and species-specific resolutions. Our study provides an epigenomic blueprint of the dog that can be used for comparative biology and medical research.
2023-01-30 | GSE203104 | GEO
Project description:Purpose: The goal of this study was to compare the microRNA transcriptomes of four high-altitude vertebrates and their low-altitude relatives for six organs (heart,liver,spleen,lung,kidney and muscle). Methods: Three adult females for each population of the five species from distinct altitudes (600 m, 2000 m, and 3000 m) were humanely killed to ameliorate suffering. A piece of tissue fragments from six organs including heart, liver, spleen, lung, kidney and skeletal muscle(longissimus muscle for pig, cattle, yak and sheep, and pectoral muscle for chicken) were used to extract total RNA. Small RNA libraries were constructed using the Illumina TruSeq Small RNA Sample Prep kit and sequenced on the Illumina HiSeq 2500. The raw data were submitted to miRDeep2.0 to detect miRNAs for each species with default parameters. Results: we detected 2,036 mature miRNAs in five species and identified 49 orthologues among vertebrate, 111 orthologues in artiodactyla and 171 orthologues in ruminant . Conclusions: We identified comparable numbers of miRNAs in each species.
2019-08-19 | GSE124418 | GEO
Project description:Transcriptomes for five species of Costus Raw sequence reads
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Project description:Global amphibian declines and extinction events are currently occurring at an unprecedented rate. While various factors are influencing these declines, one factor that is readily identifiable is disease. Specifically, the fungal pathogen Batrachochytrium dendrobatidis is thought to play a major role in amphibian declines in tropical and neotropical regions of the globe. While the effects of this chytrid fungus have been shown to be devastating, certain individuals and relict populations have shown resistance. This resistance has been attributed in part to the cutaneous microbiome. Many identified bacterial species that make up the microbiome have shown anti-B. dendrobatidis activity in vitro. One bacteria that is commonly associated as being a member of the amphibian microbiome across amphibian species and shows such anti-B. dendrobatidis activity is Serratia marcescens. Here, we look at transcriptomic shifts in gene expression of S. marcescens (high homology to strain WW4) in response to both live and heat-killed B. dendrobatidis.
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Project description:Genomes and antennal transcriptomes of five species of Eucerine bees
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