{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Junyu Bai"],"organism":["Solanum lycopersicum"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17159"],"description":["This experiment investigates FERONIA-dependent translational regulation in tomato roots under salt stress. Wild-type and feronia mutant seedlings were grown under control conditions or treated with 150 mM NaCl, and root tissues were collected from four experimental groups: WT control, WT salt-treated, fer control, and fer salt-treated, each with three biological replicates. Ribosome profiling was performed to quantify ribosome-protected fragments, ribosome occupancy, and translational efficiency. The matched RNA-seq dataset is provided as a related experiment."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Treatment - At 3–4 weeks after sowing, tomato seedlings were divided into control and salt-treatment groups. Salt-treated plants were subjected to a progressive salt treatment culminating in 150 mM NaCl. Control plants were maintained in 1/4-strength Hoagland’s medium. Root tissues were harvested after 5 days of salt treatment from each group.","Growth Protocol - Wild-type tomato (Solanum lycopersicum cv. Condine Red) and the CRISPR/Cas9-generated fer mutant line in the cv. Condine Red background were grown in a greenhouse under controlled conditions with a 16 h light/8 h dark photoperiod at 30°C during the light period and 25°C during the dark period. Plants were maintained in 1/4-strength Hoagland’s medium before treatment.","Sequencing - Ribo-seq libraries were sequenced by Guangzhou Gene Denovo Biotechnology Co., Ltd. using an Illumina sequencing platform. Libraries were sequenced in paired-end mode. Sequencing was performed to generate raw FASTQ files for each biological replicate. The sequencing hardware should be specified according to the sequencing report, for example Illumina NovaSeq 6000 if that was the instrument used.","Library Construction - Ribosome profiling libraries were constructed using a modified Ribo-seq workflow. Purified ribosome-protected fragments were subjected to 5′ phosphorylation with T4 polynucleotide kinase, sequential ligation to 3′ and 5′ adaptors, reverse transcription, and PCR amplification for 12 cycles. The final libraries were size selected by PAGE, and fragments of approximately 140 bp were recovered for sequencing.","Nucleic Acid Extraction - Ribosome profiling libraries were prepared from tomato root tissue lysates. Clarified lysates were digested with RNase I and DNase I to generate ribosome-protected fragments (RPFs). Ribosome-associated fractions were recovered using MicroSpin S-400 columns. RPFs were then extracted, followed by rRNA depletion and RNA cleanup. For matched RNA-seq libraries, total RNA was extracted from tomato roots using the RNAprep Pure Plant Kit (DP419; Tiangen Biotech, Shanghai, China) according to the manufacturer’s instructions.","Sample Collection - Root tissues were harvested from wild-type and fer tomato seedlings under control and salt-treated conditions. For each condition, roots from biologically independent seedlings were collected after 5 days of treatment, immediately frozen in liquid nitrogen, and stored at low temperature until ribosome profiling library preparation. Three biological replicates were collected for each genotype-by-treatment group."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw Ribo-seq reads were processed with fastp using paired-end merging and adapter correction. Merged reads of 25–40 nt were retained. Reads derived from rRNA were removed by aligning to tomato rRNA sequences with Bowtie allowing no mismatches. Non-rRNA reads were mapped to the Solanum lycopersicum SL4.0 reference genome with ITAG4.0 annotation using STAR with end-to-end alignment. Gene-level ribosome occupancy was quantified from CDS-overlapping reads using featureCounts, excluding multi-mapping and multi-overlap reads. Raw count matrices were normalized using the TMM method and transformed to logCPM with edgeR. Differential ribosome-occupancy analysis was performed using DESeq2. Gene-level translational efficiency was calculated as normalized ribosome occupancy divided by normalized RNA abundance using the matched RNA-seq dataset, following the deltaTE framework. The processed data files include gene-level RPF counts, normalized ribosome occupancy matrices, translational efficiency values, and differential analysis results where applicable."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq X"],"study_type":["Ribo-seq"],"species":["Solanum lycopersicum"],"pubmed_authors":["Junyu Bai"],"additional_accession":[]},"is_claimable":false,"name":"Ribo-seq of wild-type and feronia mutant tomato roots under salt stress","description":"This experiment investigates FERONIA-dependent translational regulation in tomato roots under salt stress. Wild-type and feronia mutant seedlings were grown under control conditions or treated with 150 mM NaCl, and root tissues were collected from four experimental groups: WT control, WT salt-treated, fer control, and fer salt-treated, each with three biological replicates. Ribosome profiling was performed to quantify ribosome-protected fragments, ribosome occupancy, and translational efficiency. The matched RNA-seq dataset is provided as a related experiment.","dates":{"release":"2026-06-12T00:00:00Z","modification":"2026-06-12T21:45:46.511Z","creation":"2026-06-12T14:57:15.068Z"},"accession":"E-MTAB-17159","cross_references":{"ENA":["ERP194994"],"Biostudies":["E-MTAB-17154"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0008891","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}