OzBarley: genotypic and expression data of the OzBarley elite panel

Genotyping data (HapMap file)The OzBarley germplasm was genotyped using the Infinium™ Wheat Barley 40K v1.0 BeadChip (Elite Panel) and v1.1 BeadChip (Landraces) (Illumina, San Diego, USA).In addition, RNA sequencing of the OzBarley elite panel was conducted using 4-day old seedlings germinated on filter paper (roots, embryo and coleoptile).Library preparation and sequencing was conducted at the Australian Genome Research Facility.SNP data from the chip and RNAseq data was combined and aligned to Barley cv. MorexV3.(refer to readme file for more details)Transcript abundance (cpm_count files)cpm_counts.tsv and cpm_count.xlsx contain the results of an RNA-Seq experiment conducted on 217 barley accessions. The sequence reads were aligned to the Morex v3 reference genome, followed by read counting and normalization. The read counts are expressed in CPM (counts per million reads). The final column provides gene annotations, which were obtained alongside the Morex v3 genome assembly (version Hv_Morex.pgsb.Jul2020) from GrainGenes (https://wheat.pw.usda.gov/GG3/).SNP effects (snp_description file)SNPs identified from the RNA-Seq data were combined with genotype calls obtained using the Illumina XT Wheat-Barley SNP chip. The file snp_description.csv provides information on the genomic location of each SNP and their predicted effects on genes. Variant effects were determined using the SnpEff software (https://pcingola.github.io/SnpEff/). For detailed explanations of the effect terms used, refer to Table 2 in the publication by Cingolani et al. (2012): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3679285/Supplementary Data 1A file containing the OzBarley IDs and cultivar names to match the phylogenetic network analysis presented in the OzBarley manuscript (Figure 4)