Citation: M. Schreiber et al. (2023-02-24): Grain_RawCounts.txt. Size: 35.1 MB

Abstract: RNA-sequencing data and variant call files from a collection of 209 different European two-rowed barley genotypes. The RNA-sequencing data came from six different tissues across a range of barley developmental stages: crown, root, inflorescence, peduncle, spikelet and grain. Reads were mapped against a barley reference transcriptome BaRTv2 (Coulter et al., 2022; doi:10.1111/tpj.15871) using Salmon (Patro et al., 2017; doi:10.1038/nmeth.4197). For each tissue one file containing the raw count and one file containing the transcripts per million (TPM) values are given in the folder “Gene_expression”. Variant calling of single nucleotide polymorphisms was done on the RNA-sequencing data from the six different tissues mentioned above and shallow 2x coverage whole genome shotgun sequencing (WGS). Raw reads were mapped against the Barke reference genome (Jayakodi et al., 2020; doi:10.1038/s41586-020-2947-8) using STAR (Dobin et al., 2013; doi:10.1093/bioinformatics/bts635). Variant calling of insertions or deletions (Indels) was done using the RNA-sequencing data from the six different tissues using the same Barke reference genome. Annotation was added using SnpEff (Cingolani et al., 2012; doi:10.4161/fly.19695). Two files one containing the SNP information and the other the Indel information are given in the folder “Variant_identification”. Raw data files are available through the European Nucleotide Archive under the following project numbers: PRJEB49069 (RNA-seq) / PRJEB48903 (WGS).

License: CC BY 4.0 (Creative Commons Attribution)