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. 2018 Mar 6;5:180033. doi: 10.1038/sdata.2018.33

Table 3. Experimental design for L. v. alpina clinical survival experiment, Experiment A.

Dataset Number Data Citation Number Description Number of files File names File formats Readme file Description of Readme file
Numbers of L. v. alpina frogs from each population and clutch are outlined, including details of blind randomized block design used for allocation of treatment groups (exposed frogs versus sham-exposed negative control frogs).              
1 1 Animal signalment, survival and pathogen infection intensity data from the animals in Experiment A 1 Dataset 1 Experiment A results data .csv Yes Column header descriptions
2 1 Animal signalment and pathogen infection intensity data from the animals in Experiment B 1 Dataset 2 Experiment B results data .csv Yes Column header descriptions
3 2 Raw RNA-Seq reads from skin, liver and spleen tissues of each frog sampled as part of Experiment B 362 Please refer to NCBI records (NCBI BioProject PRJNA356986) .fastq.gz No N/A
4 1 Summaries of the phred Q-score quality control data accompanying the sequence data from each tissue sample (in Dataset 3) 1 Dataset 4 Mean FastQC Quality scores .csv Yes Column header descriptions
5 1 De novo assembled transcriptomes for each tissue type from frogs in Experiment B 6 Dataset 5.1 Liver-filtered-condensed .fasta Yes Sequence identifier line descriptions for both nucleotide and amino acid sequences
        Dataset 5.2 Liver-filtered-condensed-transdecoder      
        Dataset 5.3 Skin-filtered-condensed      
        Dataset 5.4 Skin-filtered-condensed-transdecoder      
        Dataset 5.5 Spleen-filtered-condensed      
        Dataset 5.6 Spleen-filtered-condensed-transdecoder      
6 1 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) from frogs in Experiment B 3 Dataset 6.1 Liver transcriptome functionally annotated .csv Yes Column header descriptions
        Dataset 6.2 Skin transcriptome functionally annotated      
        Dataset 6.3 Spleen transcriptome functionally annotated      
7 1 Raw gene/transcript counts data for each frog tissue sample from Experiment B resulting from allocation of sequence reads to genes from the tissue-specific transcriptome assemblies 12 Dataset 7.1 Liver gene expression matrix.isoforms.counts .txt No N/A
        Dataset 7.2 Liver gene expression matrix.isoforms.TMM.EXPR      
        Dataset 7.3 Liver gene expression matrix.isoforms.TPM.not_cross_norm      
        Dataset 7.4 Liver gene expression matrix.isoforms.TPM.not_cross_norm.TMM_info      
        Dataset 7.5 Skin gene expression matrix.isoforms.counts      
        Dataset 7.6 Skin gene expression matrix.isoforms.TMM.EXPR      
        Dataset 7.7 Skin gene expression matrix.isoforms.TPM.not_cross_norm      
        Dataset 7.8 Skin gene expression matrix.isoforms.TPM.not_cross_norm.TMM_info      
        Dataset 7.9 Spleen gene expression matrix.isoforms.counts      
        Dataset 7.10 Spleen gene expression matrix.isoforms.TMM.EXPR      
        Dataset 7.11 Spleen gene expression matrix.isoforms.TPM.not_cross_norm      
        Dataset 7.12 Spleen gene expression matrix.isoforms.TPM.not_cross_norm.TMM_info      
8 3 Metabolite accumulation data from skin and liver tissues for each frog from Experiment B N/A Please refer to MetaboLights records (MetaboLights MTBLS457) N/A No N/A
9 1 Metabolite accumulation data from skin and liver tissues for each frog from Experiment B 1 Dataset 9 Metabolomics results data .csv Yes Column header descriptions and associated analyte data