Arabidopsis thaliana circadian mRNA-seq gene expression processed tables from Romanowski et al., TPJ 2020.

This dataset is an add-on for Romanowski et al., TPJ 2020 (https://doi.org/10.1111/tpj.14776) containing processed files for the circadian RNAseq data in tab delimited txt format.

Here, you can the raw counts file, the normalized CPM values, and the full JTK result (without recalculated circadian phases, just the original ones). All genes with a read density > 0.05 in at least one timepoint were considered expressed. The read density is calculated as the amount of reads divided by the effective length of a gene (total reads / length). Genes rd file is also included.

Some useful notes:
1) Counts were assigned using ASpli and the AtRTDv2 annotation (34,212 genes).
2) After filtering by rd we had a total of 18,503 expressed genes.
3) 13,256 genes passed the QL F-tests.
4) 9,127 genes were rhythmic according to JTK_cycle. 

For detailed protocols, please see Romanowski et al., TPJ 2020 (https://doi.org/10.1111/tpj.14776)

The RNA-seq raw data supporting the conclusions of this article have been deposited in ArrayExpress (Kolesnikov et al., 2015) at EMBL-EBI (www.ebi.ac.uk/arrayexpress), under accession numbers E-MTAB-7933.

All relevant custom r scripts are available at https://github.com/aromanowski/Circadian_rhythms_and_alternative_splicing