{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Zihao Zhu"],"organism":["Hordeum vulgare subsp. spontaneum"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17344"],"description":["ChIP-seq was performed to characterize histone modification landscapes and to enable comparative epigenomic analyses across the barley pangenome. Leaf tissues from seedling shoots of 10 barley genotypes were collected from plants grown under controlled conditions (16 h light/8 h dark, 20°C day/16°C night). Chromatin was crosslinked with 1% formaldehyde, quenched with glycine, and nuclei were isolated following tissue homogenization. Chromatin was sheared by focused ultrasonication and immunoprecipitated using antibodies specific to H3K4me3, H3K9ac, and H3K27me3. ChIP and input DNA libraries were sequenced as paired-end reads (2 × 151 bp) on Illumina NovaSeq platforms, with 2–3 biological replicates per genotype per histone mark."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).","Sample Collection - Leaf samples were collected 4 hours after lights-on.","Growth Protocol - Plants were grown in 35-well trays placed in growth chambers under a 16/8-hour light cycle at 20°C day/16°C night temperature for two weeks.","Sequencing - Libraries were sequenced (paired-end, 2 x 151 cycles).","Nucleic Acid Extraction - 2 g of tissue was crosslinked with 1% formaldehyde for 15 min under vacuum using the Universal Plant ChIP-seq Kit (Diagenode). Nuclei were isolated, and chromatin was sheared. For ChIP, anti-H3K4me3 (ab213224, abcam; 04-745, Millipore; C15410003, Diagenode), anti-H3K9ac (ab4441, abcam), and anti-H3K27me3 (ab6002, abcam; C15410195, Diagenode) antibodies were used."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Peak calling was performed using MACS (v3.0.0) with a q-value threshold of 0.05. ChIP-seq peaks were identified relative to matched input controls, calling narrow peaks for H3K4me3 and H3K9ac and broad peaks for H3K27me3 using a broad cutoff of 0.1. IP/input signal comparison was performed using bamCompare."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["ChIP-seq"],"species":["Hordeum vulgare subsp. spontaneum"],"pubmed_authors":["Zihao Zhu"],"additional_accession":[]},"is_claimable":false,"name":"ChIP-seq profiling of histone modifications (H3K4me3, H3K9ac, and H3K27me3) in seedling shoot tissues from 10 barley genotypes","description":"ChIP-seq was performed to characterize histone modification landscapes and to enable comparative epigenomic analyses across the barley pangenome. Leaf tissues from seedling shoots of 10 barley genotypes were collected from plants grown under controlled conditions (16 h light/8 h dark, 20°C day/16°C night). Chromatin was crosslinked with 1% formaldehyde, quenched with glycine, and nuclei were isolated following tissue homogenization. Chromatin was sheared by focused ultrasonication and immunoprecipitated using antibodies specific to H3K4me3, H3K9ac, and H3K27me3. ChIP and input DNA libraries were sequenced as paired-end reads (2 × 151 bp) on Illumina NovaSeq platforms, with 2–3 biological replicates per genotype per histone mark.","dates":{"release":"2026-07-12T00:00:00Z","modification":"2026-07-12T09:58:59.445Z","creation":"2026-07-10T15:05:58.049Z"},"accession":"E-MTAB-17344","cross_references":{"ENA":["ERP201045"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0002692","EFO_0005518","EFO_0003816","EFO_0004184"]}}