RNA-Sequencing of onion bulbs exposed to managed stress
The goal of this study was to compare differentially expressed transcripts in onion bulbs induced in response to managed stress under field conditions using transcriptome profiling (RNA-seq). The clean reads were aligned to the reference genome (a doubled haploid onion line DHCU066619 (https://www.oniongenome.wur.nl/)  and the transcriptions assembly. The read count for every transcript was determined from the findings of the mapping process. Genes identified as differentially expressed genes (DEGs) had an adjusted P-value <0.05 and an absolute log2FC?=0, as determined by DESeq2. Transcriptomic analysis of onion bulb tissue (variety Matahari) in response to nitrogen stress under optimal water identified 3092 and 2204 Differentially Expressed Genes (DEGs) unique genes under optimal nitrogen vs low nitrogen. while under sub-optimal nitrogen, 2770 and 2198 unique genes were identified under optimal nitrogen vs low nitrogen respectively. Overall design: Methods: Onion bulbs inoculated with Salmonella enterica were flash-frozen in liquid nitrogen from three independent bulbs exposed to managed stresses (nitrogen and water) at the time of harvest. The samples collected from field were used for RNA extractions. For the nitrogen stress set of samples exposed to optimal water and nitrogen (HW_HN1, HW_HN2, HW_HN3) were compared to samples collected from optimal water and sub-optimal nitrogen (HW_LN4,HW_LN5,HW_LN6). Likewise, samples collected from sub-optimal water under optimal nitrogen (LW_HN7, LW_HN8,LW_HN9) were compared to sub-optimal nitrogen (LW_LN10, LW_LN11,LW_LN123). Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount