biostudies-arrayexpressJoram DongusArabidopsis thalianaNextflow rnaseq rev 3.9https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16910This dataset identifies genes expressed in florally induced meristems of Col-0 and skrt-2 plants, in control conditions and during salt stress. It allows us to identify how skrt-2 and salt affect the timing of the floral transition, and how the floral transition itself is regulated.biostudies-arrayexpressSample Treatment - Seven days after sowing, each tray was watered with 800mL of control solution (tap water, no suppletion of NaCl) or 800 mL salt solution that contained 18.40 g NaCl. Each tray contained 21 7x7 cm pots that can take up 3.5 L of water, where the water volume varied between ~ 3 L to ~4.3 L, meaning that the NaCl concentration varied between ~75 mM and ~105 mM NaCl. Afterwards, all plants were well-watered with tap water without added NaCl, to limit salt concentrations becoming too high and excluding water-limiting stress to affect plant phenotypes.Growth Protocol - eeds were stratified in demi-water 4 °C in the dark for 2-4 days and sown directly on standard potting soil. Seeds were covered for 3-4 days with a transparent plastic cover to achieve a high and consistent humidity level and germination. Genotypes were separated from each other in a Latin square design.Library Construction - Total RNA integrity and purity were assessed using an Agilent 5400 by Novogene (UK Co. Ltd (Cambridge, UK)) and subsequently used for RNA poly-A enrichment library preparation and transcriptomeNucleic Acid Extraction - Samples were homogenized using 2 stainless steel beads in 2 mL tubes (SafeSeal; Sarstedt) in a paint shaker (Fast & Fluid) until samples were fully homogenized. RNA isolation was performed using the Universal RNA purification kit (Roboklon; EURx, Berlin, Germany). Possible DNA contaminants were eliminated with an on-column DNaseI digest.Sequencing - sequencing (150bp paired-end mode) on a NovaSeq 6000 platform (Novogene UK Co. Ltd (Cambridge, UK)).Sample Collection - Seven to nine apices per sample were harvested by hand disection between ZT 7.5 and ZT 9.5 in triplicate and snapfrozen in liquid nitrogen and stored at -70 °C.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Reads were mapped to the TAIR10 genome (retrieved: 20240308) using the Nextflow (v. 23.04.3) rnaseq pipeline (rev. 3.9; Di Tommaso et al., 2017) yielding 15-75 million reads per sample.Data Transformation - Normalisation of processed files was performed with the default settings of nextflow/rnaseq 3.9 pipeline. Specifically STAR followed by salmonMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAArabidopsis thalianaKilian DuijtsChrista TesterinkJoram DongusfalseThe effect of SAUERKRAUT and salt on the floral transition in the shoot apexThis dataset identifies genes expressed in florally induced meristems of Col-0 and skrt-2 plants, in control conditions and during salt stress. It allows us to identify how skrt-2 and salt affect the timing of the floral transition, and how the floral transition itself is regulated.2026-09-11T00:00:00Z2026-09-11T07:35:54.072Z2026-04-15T12:41:08.919ZE-MTAB-16910ERP192193EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969