biostudies-arrayexpressAgata Daszkowska-GolecHordeum vulgarehttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15043Drought poses a significant limitation to crop yield. The nuclear Cap Binding Complex (CBC), made up of CBP20 and CBP80, plays a key role in regulating pre-mRNA splicing and abscisic acid (ABA) signaling. In this study, we examined how mutations in the barley CBC genes (hvcbp20.ab, hvcbp80.b, and the double mutant hvcbp20.ab/hvcbp80.b) affect physiological and transcriptomic responses to drought stress during the booting stage and to the ABA pre-treatment, which occurred at the tillering stage and preceded drought stress. Altogether, our results highlight the nuclear CBC as a central modulator of drought responses and recovery in barley, capable of reprogramming gene expression to support enhanced stress resilience. Here we deposit control samples (plant growth in optimal conditions) collected 75 days after planting and 85 days after planting.biostudies-arrayexpressNucleic Acid Extraction - Total RNA from leaf tissue was extracted using miRvana isolation kit (ThermoFisher Scientific, USA) according to the manufacturer's guidelines. Concentration and quality were assessed using a NanoDrop spectrophotometer (ND-1000).Sequencing - Sequencing was performed on an Illumina NovaSeq 6000 at Macrogen, generating 2 × 150 bp paired-end reads, with six samples per lane utilizing an entire flow cell. The dataset included four replicates per genotype.Sample Collection - We used as an object barley plants (Hordeum vulgare (L.)), cultivar ‘Sebastian’ and its mutants TILLING hvcbp20.ab, hvcbp80.b and hvcbp20.ab/hvcbp80.b. The plants were grown in optimal water content (15% volumetric water content). The soil moisture was monitored daily using the TDR EasyTest (Institute of Agrophysics, Polish Academy of Sciences, Poland). The tissue was collected from the 3rd barley leaf from its middle part in 4 biological replicates, where each replicate included tissue from 3 independent plants.Library Construction - cDNA libraries generated using the Illumina TruSeq protocol were sequenced on an Illumina NovaSeq 6000 platform by Macrogen, producing paired-end reads of 2 × 150 bp length. Each sequencing lane contained six samples, and an entire flow cell was utilized.Growth Protocol - We used as an object barley plants (Hordeum vulgare (L.)), cultivar ‘Sebastian’ and its mutants TILLING hvcbp20.ab, hvcbp80.b and hvcbp20.ab/hvcbp80.b. The plants were grown in optimal water content (15% volumetric water content). The soil moisture was monitored daily using the TDR EasyTest (Institute of Agrophysics, Polish Academy of Sciences, Poland). The tissue was collected from the 3rd barley leaf from its middle part in 4 biological replicates, where each replicate included tissue from 3 independent plants.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - High-quality reads were aligned to the barley reference transcriptome (BaRTv2.18) with Kallisto v. 0.46.2. Differential gene expression was analyzed using 3DRNAseq within the R software environment. Read counts and transcripts per million (TPM) were derived from Kallisto outputs via the tximport R package. Transcripts and genes with low expression levels were filtered based on the mean-variance relationship, and genes were classified as expressed if they met defined thresholds for counts per million (CPM). The trimmed mean of M-values (TMM) method was applied for count normalization, and principal component analysis (PCA) revealed no notable batch effects.Sequence Alignment - High-quality reads were aligned to the barley reference transcriptome (BaRTv2.18) with Kallisto v. 0.46.2. Differential gene expression was analyzed using 3DRNAseq within the R software environment. Read counts and transcripts per million (TPM) were derived from Kallisto outputs via the tximport R package. Transcripts and genes with low expression levels were filtered based on the mean-variance relationship, and genes were classified as expressed if they met defined thresholds for counts per million (CPM). The trimmed mean of M-values (TMM) method was applied for count normalization, and principal component analysis (PCA) revealed no notable batch effects.UnknownTranscriptomicsGenomicsProteomicsMacrogenIllumina NovaSeq 6000Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in KatowiceRNA-seq of coding RNAHordeum vulgareHubert MatkowskiAgata Daszkowska-GolecfalseRNA-seq analysis of barley hvcbp20.ab, hvcbp80.b and hvcbp20.ab/hvcbp80.b under optimal conditionsDrought poses a significant limitation to crop yield. The nuclear Cap Binding Complex (CBC), made up of CBP20 and CBP80, plays a key role in regulating pre-mRNA splicing and abscisic acid (ABA) signaling. In this study, we examined how mutations in the barley CBC genes (hvcbp20.ab, hvcbp80.b, and the double mutant hvcbp20.ab/hvcbp80.b) affect physiological and transcriptomic responses to drought stress during the booting stage and to the ABA pre-treatment, which occurred at the tillering stage and preceded drought stress. Altogether, our results highlight the nuclear CBC as a central modulator of drought responses and recovery in barley, capable of reprogramming gene expression to support enhanced stress resilience. Here we deposit control samples (plant growth in optimal conditions) collected 75 days after planting and 85 days after planting.2025-12-31T00:00:00Z2025-12-31T02:02:14.841Z2025-04-17T10:38:24.524ZE-MTAB-15043ERP171768EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184