Data from: Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks

Huang Y, Chain F, Panchal M, Eizaguirre C, Kalbe M, Lenz T, Samonte I, Stoll M, Bornberg-Bauer E, Reusch TB, Milinski M, Feulner P

Date Published: January 6, 2016

DOI: http://dx.doi.org/10.5061/dryad.hq50s

 

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Title Raw expression count by HTSeq
Downloaded 36 times
Description Raw expression count data of each library for each Ensembl genes generated by HTSeq. Each column represents a library and each row represents an annotated stickleback gene from Ensembl. Description of the libraries (tissue types, habitat types, sampling locations and sex of the samples) are given in the README.txt file.
Download count_htseq.txt (6.607 Mb)
Download README.txt (2.193 Kb)
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Title EdgeR results for head kidney libraries
Downloaded 11 times
Description Differential gene expression analysis results for head kidney libraries from EdgeR, including all genes in the analysis. This file contains information on log-fold-changes (logFC) between lake and river ecotypes (positive values indicate higher expression in river and vice versa), log of average count per million reads (logCPM), likelihood ratio (LR), raw p values as well as adjusted p values (FDR).
Download edgeR_results_hk.txt (1.404 Mb)
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Title EdgeR results for spleen libraries
Downloaded 13 times
Description Differential gene expression analysis results for spleen libraries from EdgeR, including all genes in the analysis. This file contains information on log-fold-changes between lake and river ecotypes (positive values indicate higher expression in river and vice versa), log of average count per million reads (logCPM), likelihood ratio (LR), raw p values as well as adjusted p values (FDR).
Download edgeR_results_sp.txt (1.444 Mb)
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Title GO enrichment analyses in head kidney
Downloaded 21 times
Description Results of Gene Ontology (GO) enrichment analyses among DE genes in the head kidney.
Download topGO_hk.xlsx (55.03 Kb)
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Title GO enrichment analyses in spleen
Downloaded 18 times
Description Results of Gene Ontology (GO) enrichment analyses among DE genes in the spleen.
Download topGO_sp.xlsx (55.83 Kb)
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When using this data, please cite the original publication:

Huang Y, Chain F, Panchal M, Eizaguirre C, Kalbe M, Lenz T, Samonte I, Stoll M, Bornberg-Bauer E, Reusch TB, Milinski M, Feulner P (2016) Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks. Molecular Ecology, 25(4):943–958. http://dx.doi.org/ 10.1111/mec.13520

Additionally, please cite the Dryad data package:

Huang Y, Chain F, Panchal M, Eizaguirre C, Kalbe M, Lenz T, Samonte I, Stoll M, Bornberg-Bauer E, Reusch TB, Milinski M, Feulner P (2016) Data from: Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.hq50s
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