{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Joram Dongus"],"organism":["Arabidopsis thaliana"],"software":["Nextflow rnaseq rev 3.9"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16910"],"description":["This 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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample 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 transcriptome","Nucleic 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence 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 salmon"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Arabidopsis thaliana"],"pubmed_authors":["Kilian Duijts","Christa Testerink","Joram Dongus"],"additional_accession":[]},"is_claimable":false,"name":"The effect of SAUERKRAUT and salt on the floral transition in the shoot apex","description":"This 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.","dates":{"release":"2026-09-11T00:00:00Z","modification":"2026-09-11T07:35:54.072Z","creation":"2026-04-15T12:41:08.919Z"},"accession":"E-MTAB-16910","cross_references":{"ENA":["ERP192193"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}