Data from: Survival, gene and metabolite responses of Litoria verreauxii alpina frogs to fungal disease chytridiomycosis
Grogan, Laura, Griffith University
Mulvenna, Jason, QIMR Berghofer Medical Research Institute
Gummer, Joel P. A., Murdoch University
Scheele, Benjamin C., James Cook University
Berger, Lee, James Cook University
Cashins, Scott D., James Cook University
McFadden, Michael S., Taronga Conservation Society Australia
Harlow, Peter, Taronga Conservation Society Australia
Hunter, David A., NSW Office of Environment & Heritage
Trengove, Robert D., Murdoch University
Skerratt, Lee F., James Cook University
Published Feb 01, 2019 on Dryad.
https://doi.org/10.5061/dryad.t1p7c
Cite this dataset
Grogan, Laura et al. (2019). Data from: Survival, gene and metabolite responses of Litoria verreauxii alpina frogs to fungal disease chytridiomycosis [Dataset]. Dryad. https://doi.org/10.5061/dryad.t1p7c
Abstract
PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN ANOTHER PUBLICATION. PLEASE SEE http://dx.doi.org/10.1111/mec.14493. 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) from multiple populations (one evolutionarily naïve to chytridiomycosis) 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.
Usage notes
Dataset 1 Experiment A results data
Dataset 1 consists of animal signalment, survival and pathogen infection intensity data from the animals in Experiment A. These data are contained in Dataset 1, as a single comma-separated file (.csv format), entitled ‘Dataset 1 Experiment A results data’ [Data Citation 1]. Each row below the header represents an individual frog (n = 353, from the original 355 minus two whose data were removed due to mortality pre-exposure), and columns (n = 55) contain frog identifier and treatment group information, signalment and measurement data, raw qPCR results, and length of survival data. Full descriptions of the column headers are contained in the associated readme file. Please see the associated metadata records in Supplementary File 1 for full details of study subjects and swab samples collected.
Dataset 2 Experiment B results data
Dataset 2 consists of animal signalment and pathogen infection intensity data from the animals in Experiment B. These data are contained in Dataset 2, as a single comma-separated file (.csv format), entitled ‘Dataset 2 Experiment B results data’ [Data Citation 1]. Each row below the header represents an individual frog (n = 61, from the original 51 frogs in this experiment plus the 10 frogs that were obtained from Experiment A and sampled when moribund at 28-30 days post exposure). Columns (n = 27) contain frog identifier and treatment group information, signalment and measurement data, and qPCR results data. Full descriptions of the column headers are contained in the associated readme file. Please see the associated metadata records in Supplementary File 1 for full details of study subjects and swab samples collected.
Dataset 4 Sequencing quality control data
Dataset 4 consists of a summary of the phred Q-score quality control data accompanying the sequence data from each tissue sample (described above). These data are contained in Dataset 4 as a single comma-separated file (.csv format). Descriptions of the column headers are contained in the associated readme file.
Dataset 5.1 Liver-filtered-condensed
Dataset 5 consists of de novo assembled transcriptomes for each tissue type from frogs in Experiment B (n = 61). These data are contained in Dataset 5, as six individual .fasta text files, including both nucleotide sequence assembly files and amino acid sequence assembly files (translated using TransDecoder) for each of the three tissue types (skin, liver and spleen) [Data Citation 1]. Descriptions of the sequence identifier lines are contained in the associated readme file.
Dataset 5.2 Liver-filtered-condensed-transdecoder
Dataset 5 consists of de novo assembled transcriptomes for each tissue type from frogs in Experiment B (n = 61). These data are contained in Dataset 5, as six individual .fasta text files, including both nucleotide sequence assembly files and amino acid sequence assembly files (translated using TransDecoder) for each of the three tissue types (skin, liver and spleen) [Data Citation 1]. Descriptions of the sequence identifier lines are contained in the associated readme file.
Dataset 5.3 Skin-filtered-condensed
Dataset 5 consists of de novo assembled transcriptomes for each tissue type from frogs in Experiment B (n = 61). These data are contained in Dataset 5, as six individual .fasta text files, including both nucleotide sequence assembly files and amino acid sequence assembly files (translated using TransDecoder) for each of the three tissue types (skin, liver and spleen) [Data Citation 1]. Descriptions of the sequence identifier lines are contained in the associated readme file.
Dataset 5.4 Skin-filtered-condensed-transdecoder
Dataset 5 consists of de novo assembled transcriptomes for each tissue type from frogs in Experiment B (n = 61). These data are contained in Dataset 5, as six individual .fasta text files, including both nucleotide sequence assembly files and amino acid sequence assembly files (translated using TransDecoder) for each of the three tissue types (skin, liver and spleen) [Data Citation 1]. Descriptions of the sequence identifier lines are contained in the associated readme file.
Dataset 5.5 Spleen-filtered-condensed
Dataset 5 consists of de novo assembled transcriptomes for each tissue type from frogs in Experiment B (n = 61). These data are contained in Dataset 5, as six individual .fasta text files, including both nucleotide sequence assembly files and amino acid sequence assembly files (translated using TransDecoder) for each of the three tissue types (skin, liver and spleen) [Data Citation 1]. Descriptions of the sequence identifier lines are contained in the associated readme file.
Dataset 5.6 Spleen-filtered-condensed-transdecoder
Dataset 5 consists of de novo assembled transcriptomes for each tissue type from frogs in Experiment B (n = 61). These data are contained in Dataset 5, as six individual .fasta text files, including both nucleotide sequence assembly files and amino acid sequence assembly files (translated using TransDecoder) for each of the three tissue types (skin, liver and spleen) [Data Citation 1]. Descriptions of the sequence identifier lines are contained in the associated readme file.
Dataset 6.1 Liver transcriptome functionally annotated
Dataset 6 consists of functional annotation data (from the Gene Ontology [GO] consortium, Enzyme Code and Inter Pro databases) for each gene assembled, across the three tissue types (skin, liver and spleen). These data are contained in Dataset 6, as three individual comma-separated files (.csv format) [Data Citation 1]. Full descriptions of the column headers are contained in the associated readme file.
Dataset 6.2 Skin transcriptome functionally annotated
Dataset 6 consists of functional annotation data (from the Gene Ontology [GO] consortium, Enzyme Code and Inter Pro databases) for each gene assembled, across the three tissue types (skin, liver and spleen). These data are contained in Dataset 6, as three individual comma-separated files (.csv format) [Data Citation 1]. Full descriptions of the column headers are contained in the associated readme file.
Dataset 6.3 Spleen transcriptome functionally annotated
Dataset 6 consists of functional annotation data (from the Gene Ontology [GO] consortium, Enzyme Code and Inter Pro databases) for each gene assembled, across the three tissue types (skin, liver and spleen). These data are contained in Dataset 6, as three individual comma-separated files (.csv format) [Data Citation 1]. Full descriptions of the column headers are contained in the associated readme file.
Dataset 7.1 Liver matrix.isoforms.counts
Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
Dataset 7.2 Liver matrix.isoforms.TMM.EXPR
Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
Dataset 7.3 Liver matrix.isoforms.TPM.not_cross_norm
Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
Dataset 7.4 Liver matrix.isoforms.TPM.not_cross_norm.TMM_info
Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
Dataset 7.5 skin matrix.isoforms.counts
Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
Dataset 7.6 Skin matrix.isoforms.TMM.EXPR
Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
Dataset 7.7 Skin matrix.isoforms.TPM.not_cross_norm
Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
Dataset 7.8 Skin matrix.isoforms.TPM.not_cross_norm.TMM_info
Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
Dataset 7.9 Spleen matrix.isoforms.counts
Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
Dataset 7.10 Spleen matrix.isoforms.TMM.EXPR
Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
Dataset 7.11 Spleen matrix.isoforms.TPM.not_cross_norm
Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
Dataset 7.12 Spleen matrix.isoforms.TPM.not_cross_norm.TMM_info
Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
Dataset 9 Metabolomics results data
Dataset 9 contains the metabolite accumulation data from skin and liver tissues for each frog from Experiment B (n = 61). These data have been scaled by dividing by the summed ion signal (total ion chromatogram). These data are contained as a single comma-separated file (.csv format) in Dataset 9 [Data Citation 1], with full descriptions of the column headers (and associated analyte data) contained in the associated readme file. Please see the associated metadata records in Supplementary File 1 for full details of study subjects and tissue samples collected for the metabolomics work.
Location
Australia