Oregon Spotted Frog Microbiome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB35123 | ENA |
REPOSITORIES: ENA
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Project description:Both spotted long oligonucleotide arrays and Affymetrix GeneChips were used to measure differential gene expression in two RNA samples (K562 erythroleukemia RNA and the Stratagene Universal Human Reference RNA). For Affymetrix technology, the two RNAs were analyzed separately. There are two replicates for K562 RNA (GSM4843 and GSM4844) and three for the Stratagene Universal reference (GSM4845-GSM4847). Two types of spotted long oligonucleotide arrays were used. These arrays were used to do two-color hybridizations to directly compare K562 and Universal reference RNAs. One array (GPL273) was made with probes from the Operon Human Genome Oligo Set Version 1. These arrays were used with unamplified cDNA probes (6 replicates, GSM4848-GSM4853), with aRNA probes produced by one round of T7 RNA polymerase-based amplification (6 replicates, GSM4854-GSM4859), and with aRNA probes produced by two rounds of amplification (2 replicates, GSM4860-GSM4861). Keywords: parallel sample
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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.
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