Sugar signal manipulation by T6P for yield on wheat grain - whole grain RNA-seq

Trehalose 6-phosphate (T6P) is a powerful internal sugar signal in plants yet cannot be directly added nor fully genetically controlled. A timed microdose of a plant-permeable T6P signalling precursor, DMNB-T6P, causes substantial yield improvements. This repository contains normalised counts table for a RNA-seq of wheat (Triticum aestivum) whole grains after spray with mock/DMNB-T6P. DESeq2 normalised count table for raw reads deposited in ncbi SRA under Bioproject PRJNXXXX. Related manuscript submitted to XXX. (...) Following RNA integrity analysis and quantitation (Bioanalyser; Agilent, USA), poly-A enriched cDNA libraries were generated and sequenced on an Illumina Novaseq 6000 sequencing platform generating 30–50 million 150 bp paired-end reads per sample. Low-quality reads and adaptor sequences were removed with Trimmomatic (trimmomatic-0.39.jar PE ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True TRAILING:30 MINLEN:40). The reads were aligned to the wheat reference genome (Triticum aestivum iwgsc_refseqv2.1 using HISAT2/2.2.1-foss-2019b with default parameters and converted to Bam format with SAMtools. Gene abundance was quantified using featureCounts with the High Confidence iwgsc_refseqv2.1 annotation (counting only primary alignments of read pairs with a quality cut-off of 10). Raw counts were normalized using the trimmed mean of M-values method by DESeq2.Associated RNA-seq raw reads submitted to ncbi SRA under BioProject PRJNXXX. Supporting funding not recognised by Zenodo/OPENAire - BB/P016855/1 Designing Future Wheat Institute Strategic Programme by UKRI-BBSRC (UK)