biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsMallikarjuna rao KoviIllumina NovaSeq 6000TruSeq RNA Sample Prep KitRNA-seq of coding RNAPhleum pratensePhleum pratensehttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14732The experiment was aimed at studying gene expression differences between three temporal populations of two timothy cultivars; Engmo (Early=1988, Mid=2003 & Current=2020) and Noreng (Early=1998, Mid=2010 & Current=2020), under freezing stress and Ice encasement stress. The idea is when the temporally separated populations; the ancestor and its descendant populations, were subjected to similar stress conditions the gene expression differences between populations could be due to plasticity or adaptation and the non-random changes in gene expression could be indicative of adaptative responses. The cold acclimated samples were used as controls in both freezing and ice encasement comparisonsbiostudies-arrayexpressGrowth Protocol - does not applySequencing - The pair-end sequencing was carried out in a NovaSeq PE150 (Illumina, CA, USA) using the TruSeq SBS KIT-HS V3 (Illumina, CA, USA).Sample Collection - Plants from all temporal seedlots of Engmo and Norneg were cold acclimated under ambient light conditions, first for 6 weeks at 9°C, followed by 2 weeks at 6°C and finally 2 weeks at 2°C under 12h light ( 55 PPFD). Freezing stress samples were transfered to freezers the temperature was lowered from 2°C to -3°C by 1°C h−1 and were kept at -3°C for ~ 12 hrs to avoid supercooling. After that the temperatures were lowered by 1°C h−1 from -3°C to -10°C and by 3°C until the pre-set temperatures were reached, i.e. -12, -15, -18, -21, -24, -27°C. batches of samples were taken at the predetermined temperatures flash-frozen for RNA extraction. The ice encasement samples were placed in a polyethyene container and filled with ice and cold water and kept in freezing rooms and batches of plants were withdrawn at 22,36, 54, 68, 75 and 82 days. The sampled plant material from freezing and ice encasement tests were crushed with mortar and pistel and the ground plant material is used for RNA extractionLibrary Construction - The libraries were prepared according to the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA)Nucleic Acid Extraction - RNA extraction was carried out using Qiagen RNeasy Plant Mini kit according to manufacturar guidelinesOrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesMallikarjuna rao KovifalseGene expression differences under freezing and ice encasement stress in between temporal populationsThe experiment was aimed at studying gene expression differences between three temporal populations of two timothy cultivars; Engmo (Early=1988, Mid=2003 & Current=2020) and Noreng (Early=1998, Mid=2010 & Current=2020), under freezing stress and Ice encasement stress. The idea is when the temporally separated populations; the ancestor and its descendant populations, were subjected to similar stress conditions the gene expression differences between populations could be due to plasticity or adaptation and the non-random changes in gene expression could be indicative of adaptative responses. The cold acclimated samples were used as controls in both freezing and ice encasement comparisons2025-09-01T00:00:00Z2025-09-01T01:02:25.465Z2025-01-02T16:06:05.029ZE-MTAB-14732ERP167453EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003738EFO_0004184