{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Agata Daszkowska-Golec"],"organism":["Hordeum vulgare"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15052"],"description":["Drought 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. The mutants exhibited both common and unique mechanisms of drought adaptation. Transcriptome analysis showed that loss of HvCBP80 function markedly suppressed gene transcription and splicing but activated photosynthesis-associated genes, leading to improved photosynthetic performance under both normal and drought conditions. In contrast, HvCBP20 mutation enhanced the expression of ABA-responsive genes and sustained stress-related signaling. On a physiological level, hvcbp20.ab mutants maintained higher stomatal conductance despite having fewer stomata, while hvcbp80.b mutants exhibited reduced conductance under optimal conditions but formed wider stomata during drought. Although these mutations improved certain drought avoidance traits and photosynthetic capacity, they did not translate into gains in yield-related characteristics. 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 plant samples after drought stress treatment and after rewatering"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Treatment - As the object, we used barley plants (Hordeum vulgare (L.)), cultivar ‘Sebastian’ and its mutants TILLING hvcbp20.ab, hvcbp80.b and hvcbp20.ab/hvcbp80.b. Plants were grown under drought stress during which soil moisture was reduced to 1.5% volumetric water content. Drought stress lasted 10 days and was followed by a rehydration period. Soil moisture was monitored daily using TDR EasyTest (Institute of Agrophysics PAS, 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. Tissue collected after drought stress (75 days after planting) and after rehydration (85 days after planting)","Nucleic 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 - As the object, we used barley plants (Hordeum vulgare (L.)), cultivar ‘Sebastian’ and its mutants TILLING hvcbp20.ab, hvcbp80.b and hvcbp20.ab/hvcbp80.b. Plants were grown under drought stress during which soil moisture was reduced to 1.5% volumetric water content. Drought stress lasted 10 days and was followed by a rehydration period. Soil moisture was monitored daily using TDR EasyTest (Institute of Agrophysics PAS, 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. Tissue collected after drought stress (75 days after planting) and after rehydration (85 days after planting)","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 - As the object, we used barley plants (Hordeum vulgare (L.)), cultivar ‘Sebastian’ and its mutants TILLING hvcbp20.ab, hvcbp80.b and hvcbp20.ab/hvcbp80.b. Plants were grown under drought stress during which soil moisture was reduced to 1.5% volumetric water content. Drought stress lasted 10 days and was followed by a rehydration period. Soil moisture was monitored daily using TDR EasyTest (Institute of Agrophysics PAS, 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. Tissue collected after drought stress (75 days after planting) and after rehydration (85 days after planting)"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data 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."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Macrogen","Illumina NovaSeq 6000","Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice/ Thermo Fisher Scientific","Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice"],"study_type":["RNA-seq of coding RNA"],"species":["Hordeum vulgare"],"pubmed_authors":["Hubert Matkowski","Agata Daszkowska-Golec"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq analysis of barley (Hordeum vulgare) single mutants in genes encoding barley CBC (HvCBP20, HvCBP80) and a double mutant in both genes encoding barley CBC in response to drought stress applied at the booting stage and subsequent rewatering","description":"Drought 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. The mutants exhibited both common and unique mechanisms of drought adaptation. Transcriptome analysis showed that loss of HvCBP80 function markedly suppressed gene transcription and splicing but activated photosynthesis-associated genes, leading to improved photosynthetic performance under both normal and drought conditions. In contrast, HvCBP20 mutation enhanced the expression of ABA-responsive genes and sustained stress-related signaling. On a physiological level, hvcbp20.ab mutants maintained higher stomatal conductance despite having fewer stomata, while hvcbp80.b mutants exhibited reduced conductance under optimal conditions but formed wider stomata during drought. Although these mutations improved certain drought avoidance traits and photosynthetic capacity, they did not translate into gains in yield-related characteristics. 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 plant samples after drought stress treatment and after rewatering","dates":{"release":"2026-01-31T00:00:00Z","modification":"2026-01-31T02:02:01.698Z","creation":"2025-04-17T10:41:20.806Z"},"accession":"E-MTAB-15052","cross_references":{"ENA":["ERP171769"],"Biostudies":["E-MTAB-15043"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}