A comparative transcriptomic resource for the root cold response of boreal trees across the angiosperm-gymnosperm divide: processed data and analysis outputs

This item holds the processed data and analysis outputs of a comparative study of the root response to cold in six genotypes: Norway spruce (Picea abies), Scots pine (Pinus sylvestris), silver birch (Betula pendula), aspen (Populus tremula) and the Arabidopsis thaliana ecotypes Col-0 and Ost-0 (Osthammar). Fine roots were sampled before and 6 h, 24 h, 3 d and 10 d after transfer to 5 degrees C (133 RNA-seq samples). The data include gene expression and differential expression for every genotype, orthology, comparative co-expression (ComPlEx) results for all 15 genotype pairs, the conserved co-expression core (133 orthogroups) with orthology and sample-stability labels, per-genotype co-expression networks, Gene Ontology and transcription-factor annotation, and the Salmon quantification behind the counts. They are provided both as R objects and as tab-separated text tables, with a browser page (explore.html) that needs no installation. Unpack the archive: tar -xzf data.tar.gz. Then start with README_RESOURCE.md in the unpacked folder. To look up a gene, open explore.html in a web browser. The tab-separated tables in data/open/ hold the same content as the R objects and can be read with any software; DATA_DICTIONARY.md describes every table and column, and USAGE_EXAMPLES.md gives worked examples in R and Python. The R objects (.RData, .rda, .RDS) need R (https://www.r-project.org); the DESeq2 objects need the Bioconductor package DESeq2.