{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Matteo Buti"],"organism":["Fragaria x ananassa"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14796"],"description":["This study investigates the molecular mechanisms of cold stress tolerance in two strawberry cultivars: ‘Queen Elisa,’ a highly cold-tolerant variety, and ‘Camarosa,’ a semi-sensitive variety. Using RNA-Seq analysis, we identified key genes and pathways involved in the cold stress response, providing insights into the genetic and molecular basis of cold tolerance in strawberries. These findings highlight potential targets for improving crop resilience to abiotic stress."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Two biological replicates were used for each treatment, with each biological replicate consisting of 8 plants. RNA extraction was performed from 50-100 mg of leaves ground with a pestle and mortar in liquid nitrogen using the RNeasy Plant Mini kit (Qiagen, Hilden, Germany). RNA quality was determined using RNA 6000 nano kit on Agilent 2100 Bioanalyzer (Bio-Rad, Hercules, California, USA).","Library Construction - Eight libraries were obtained using TruSeq Stranded mRNA Library Prep (Illumina, San Diego, California, USA) and TruSeq RNA Single Indexes (two libraries for each treatment).","Growth Protocol - The plants were collected as current-year runners from the Kurdistan Agricultural and Natural Resources Research and Education Center, Iran. Runners were planted in plastic pots filled with a mixture of one part decomposed manure, one part sand, and two parts garden soil, and grown in a greenhouse under a 16/8 h (day/night) photoperiod at 25°C until well-established. During the experiment, the plants were regularly watered as needed. Due to the initial weak condition of the plants, additional fertilization was applied with an NPK 20-20-20 fertilizer as a foliar spray twice with a one-week interval between applications.","Sample Treatment - Some pots were transferred for 24 hours to a cold chamber set at 4°C to induce cold stress.","Sequencing - Library sequencing was performed using NovaSeq 6000 S1 Reagent Kit (100 cycles, 2 x 100+10+10 bp parameters) on Illumina NovaSeq 6000 platform. DNA sequencing was done in paired-end mode with a read length of 150 nucleotides. All the libraries were run in a single flow cell following Illumina’s standard procedure in XP mode.","Sample Collection - Harvested strawberry leaves were immediately frozen in liquid nitrogen, and stored at -80°C for further analysis"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - EdgeR package was used to filter out unexpressed or poorly expressed transcript (a transcript was considered to be ‘active’ if the reads per million mapping to that gene were >1 in at least two libraries), and to normalize the RNA libraries depending on their dimension and assigning a CPM value for each active transcript and for each RNA library.","Sequence Alignment - After the adaptor sequences, low-quality bases and sequence shorter than 40 bases were removed using Trimmomatic v0.39, the clea RNA reads were mapped to the ASM33114v1 reference assembly (cultivar CDC Frontier) retrieved from NCBI RefSeq using HiSat2 v2.2.1 with default parameters. Read counts were generated from alignment files using the featureCounts v2.0.3 software with default parameters, according to the transcripts predicted on the reference genome."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Fragaria x ananassa"],"pubmed_authors":["Matteo Buti"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptomic responses to cold stress in cold-semi-sensitive and cold-tolerant strawberry varieties","description":"This study investigates the molecular mechanisms of cold stress tolerance in two strawberry cultivars: ‘Queen Elisa,’ a highly cold-tolerant variety, and ‘Camarosa,’ a semi-sensitive variety. Using RNA-Seq analysis, we identified key genes and pathways involved in the cold stress response, providing insights into the genetic and molecular basis of cold tolerance in strawberries. These findings highlight potential targets for improving crop resilience to abiotic stress.","dates":{"release":"2025-11-19T00:00:00Z","modification":"2025-11-19T15:46:23.32Z","creation":"2025-01-29T17:31:37.952Z"},"accession":"E-MTAB-14796","cross_references":{"ENA":["ERP168785"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}