biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsEwa SybilskaAgilent 2100 BioanalyzerReal Time qPCR System, ThermocyclerGrowth chamber, fridgeIllumina NovaSeq 6000Leica CM3050 S (cryostat), Leica Microsystems (microscope)spatial transcriptomics by high-throughput sequencingHordeum vulgare subsp. vulgareHordeum vulgare subsp. vulgarehttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14835The spatial transcriptomic analysis of barley embryos in response to 75 µM ABA was investigated using Visium Spatial Transcriptomics (10×Genomics) technology. Embryo sections were collected from wild-type 'Sebastian' and a double mutant hvcbp20.ab/hvcbp80.b impaired in both subunits of the Cap-Binding Complex (CBC): CBP20 and CBP80 at 1 day after imbibition (DAI) under control and 75 µM ABA conditions. Cryosectioned tissues were stained, mounted on Visium slides, and processed for spatial gene expression profiling. Sequencing was performed on an Illumina NovaSeq 6000 platform (paired-end, 151 bp). The data were aligned to the barley reference genome (cv. MorexV3) and used to identify differentially expressed genes (DEGs) across six distinguished embryonic regions: coleoptile, cotyledon, mesocotyl, plumule, scutellum, and radicle. The dataset provides insights into the spatial regulation of ABA-responsive genes in embryos during barley seed germination.biostudies-arrayexpressSample Treatment - Seeds were sterilized in a 20% sodium hypochlorite solution for 20 minutes and then thoroughly washed three times with sterile water for 5 minutes. After sterilization, seeds were placed in Petri dishes (⌀ = 90 mm) on three layers of Whatman filters with 5 ml of distilled water (control) or a distilled water containing 75 µM ABA solution (cis–trans-abscisic acid; Sigma-Aldrich, catalog no. 862169). The seeds were stratified in darkness at 4°C for 4 days and then transferred to a growth chamber (22°C, 16-h-light/8-h darkness, 200 μmol/m−2 s−1 illumination).Sequencing - Sequencing was performed on an Illumina NovaSeq 6000 platform in paired-end (PE) mode (151 bp). Spatial transcriptomics data were processed using Space Ranger v3.1.0, which aligned reads to the barley reference genome (MorexV3_pseudomolecules_assembly; Mascher et al., 2021) and assigned them to spatial barcodes.Nucleic Acid Extraction - RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. RNA integrity was assessed using an Agilent 2100 Bioanalyzer to determine the RNA Integrity Number (RIN).Sample Collection - We followed the protocol described in Peirats-Llobet et al. (2023). At 1 DAI (days after imbibition), embryos were isolated from the germinating seeds using a scalpel, and the embryonic root was removed. The embryos were embedded in an optimal cutting temperature (OCT) medium and frozen in an isopentane bath on dry ice. The frozen samples were stored at –80°C until further processing. Sections of 10 µm thickness were prepared using a cryostat (Leica CM3050 S) at –18°C. Two control embryo sections and three ABA embryo sections were placed on Visium Spatial Gene Expression Slide. Slides were fixed in chilled methanol for 30 min in –20°C. After fixation, sections were stained for 5 min with 0.1% Safranin O (Sigma-Aldrich, cat. no. S8884-25G) in 50% ethanol. The sections were then washed in an alcohol series (50%, 70%, 100%) for 1 min . Slides were imaged in the bright field using a light microscope (Leica DS5500) for downstream spatial transcriptomic analysis.Library Construction - cDNA libraries were prepared using the Visium Spatial Gene Expression protocol (10x Genomics). Poly-A mRNA was captured and reverse-transcribed to generate cDNA, which was subsequently amplified and indexed for sequencing.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesEwa SybilskaAgata Daszkowska-GolecfalseRNA-seq data of barley embryos of wild-type ‘Sebastian’ and double mutant hvcbp20.ab/hvcbp80.b under control conditions and in the presence of 75 µM ABAThe spatial transcriptomic analysis of barley embryos in response to 75 µM ABA was investigated using Visium Spatial Transcriptomics (10×Genomics) technology. Embryo sections were collected from wild-type 'Sebastian' and a double mutant hvcbp20.ab/hvcbp80.b impaired in both subunits of the Cap-Binding Complex (CBC): CBP20 and CBP80 at 1 day after imbibition (DAI) under control and 75 µM ABA conditions. Cryosectioned tissues were stained, mounted on Visium slides, and processed for spatial gene expression profiling. Sequencing was performed on an Illumina NovaSeq 6000 platform (paired-end, 151 bp). The data were aligned to the barley reference genome (cv. MorexV3) and used to identify differentially expressed genes (DEGs) across six distinguished embryonic regions: coleoptile, cotyledon, mesocotyl, plumule, scutellum, and radicle. The dataset provides insights into the spatial regulation of ABA-responsive genes in embryos during barley seed germination.2025-07-31T00:00:00Z2025-02-13T23:32:59.433Z2025-02-13T23:32:59.433ZE-MTAB-14835ERP169224EFO_0002944EFO_0004170EFO_0030005EFO_0005518EFO_0004184EFO_0003969