DOI: 10.5061/dryad.t1p7c
title: Data from: Survival, gene and metabolite responses of Litoria verreauxii alpina frogs to fungal disease chytridiomycosis

description: 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.
description: Dataset 1 Experiment A
 results dataDataset 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 dataDataset 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 dataDataset 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-condensedDataset 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-transdecoderDataset 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-condensedDataset 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-transdecoderDataset 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-condensedDataset 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-transdecoderDataset 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 annotatedDataset 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 annotatedDataset 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 annotatedDataset 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.countsDataset 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.EXPRDataset 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_normDataset 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_infoDataset 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.countsDataset 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.EXPRDataset 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_normDataset 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_infoDataset 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.countsDataset 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.EXPRDataset 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_normDataset 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_infoDataset 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 dataDataset 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.