README - ENLIGHTEN DEPOSIT - RESEARCH DATA

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MANUSCRIPT: Alternative splicing and gene expression play contrasting roles in the parallel phenotypic evolution of a salmonid fish

AUTHORS: Arne Jacobs & Kathryn R. Elmer

Journal: Molecular Ecology

Preprint: Alternative splicing and gene expression play contrasting roles in the parallel phenotypic evolution of a salmonid fish (2020) bioRxiv; doi: https://doi.org/10.1101/2020.05.11.087973

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All data were aligned to the Salvelinus alpinus genome assembly 'ASM291031v2' and analysed together with the corresponding Annotation Release 101.


Datasets

1.  Charr_RNAseq_ASM291031v2_filtered.vcf: VCF file containing the filtered SNP dataset called from genome-aligned RNA-seq data for all 24 individuals from all three lakes (Awe, Tay and Dughaill). The filtering is described in the Methods section of the manuscript.

2.  AllPops_htseq_readcounts_raw.zip: A zip-compressed folder containing text files with the raw transcript counts for each individual in the study as produced by HTSEQ-count. These files served as input for the gene expression analysis in DESeq2.

3.  AllPops_DESeq2_sample_table.csv: CSV file containing sample information (Name, Lake, Ecotype) for each individual. This file was used for the DESeq2 analysis.

4.  AllPops_ExonCounts_combined_raw.csv: CSV file with raw exon counts produced using a modified HTSeq-count script provided with DEXseq. This file served as input for the exon usage analysis in DEXseq. 

5.  AllPops_combined_intronCounts_leafcutter_perind_numers.counts.gz: Gzipped text file with raw intron counts produced by leafcutter for introns detected across all 24 individuals from Awe, Tay and Dughaill.

6.  AllPops_combined_leafcutter_ds_cluster_significance.txt: Text file with the differential splicing results between benthic and pelagic ecotypes from leafcutter for all populations combined.

7.  AllPops_combined_leafcutter_ds_effect_sizes.txt: Text file with the differential splicing effect sizes (∆PSI)between benthic and pelagic ecotypes from leafcutter for all populations combined.

8.  Awe_intronCounts_leafcutter_perind_numers.counts.gz: Gzipped text file with raw intron counts produced by leafcutter for introns detected across individuals in Awe.

9.  Awe_leafcutter_ds_cluster_significance.txt: Text file with the differential splicing results between benthic and pelagic ecotypes in Awe as produced by leafcutter.

10. Awe_leafcutter_ds_effect_sizes.txt: Text file with the differential splicing effect sizes between benthic and pelagic ecotypes in Awe as produced by leafcutter.

11. Tay_intronCounts_leafcutter_perind_numers.counts.gz: Gzipped text file with raw intron counts produced by leafcutter for introns detected across individuals in Tay.

12. Tay_leafcutter_ds_cluster_significance.txt: Text file with the differential splicing results between benthic and pelagic ecotypes in Tay as produced by leafcutter.

13. Tay_leafcutter_ds_effect_sizes.txt: Text file with the differential splicing effect sizes between benthic and pelagic ecotypes in Tay as produced by leafcutter.

14. Dughaill_intronCounts_leafcutter_perind_numers.counts.gz: Gzipped text file with raw intron counts produced by leafcutter for introns detected across individuals in Dughaill.

15. Dughaill_leafcutter_ds_cluster_significance.txt: Text file with the differential splicing results between benthic and pelagic ecotypes in Dughaill as produced by leafcutter.

16. Dughaill_leafcutter_ds_effect_sizes.txt: Text file with the differential splicing effect sizes between benthic and pelagic ecotypes in Dughaill as produced by leafcutter.

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The data in this repository can be freely used by anyone, but please cite the relevant manuscript:  the final manuscript (no DOI yet, but you can find it under the provided title) or the preprint (see details above).