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. <br> 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 &gt; 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:<br> 1) Counts were assigned using ASpli and the AtRTDv2 annotation (34,212 genes).<br> 2) After filtering by rd we had a total of 18,503 expressed genes.<br> 3) 13,256 genes passed the QL F-tests.<br> 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