1. ABOUT THE DATASET ------------ Title: ERUCA VESICARIA SUBSP. SATIVA RNA-SEQ GENE EXPRESSION AND ANNOTATION Creator(s): LUKE BELL (https://orcid.org/0000-0003-2895-2030) Organisation(s): UNIVERSITY OF READING Rights-holder(s): UNIVERSITY OF READING Publication Year: 2023 Description: This data file contains the full gene expression values (fpkm) of 121 Eruca vesicaria subsp. sativa samples, obtained by RNAseq (performed by Novogene UK Ltd., Cambridge, UK). Plants were grown in two field trials, one in Rome, Italy, and the other in Dorchester, UK. Six E. vesicaria cultivars were sampled across two consecutive harvests (first and second cut) two weeks apart, and again across two shelf life time points (D0 and D5). The file contains expression values for 49,487 genes, their relative positions on the E. vesicaria reference genome (https://www.ncbi.nlm.nih.gov/bioproject/PRJEB50993), their strand orientation, length, and annotation. Cite as: Bell, L. (2023): ERUCA VESICARIA SUBSP. SATIVA RNA-SEQ GENE EXPRESSION AND ANNOTATION. University of Reading. Dataset. Related publication: Bell, L., Chadwick, M., Puranik, M., Jasper, J., Hasted, A., Tudor, R., Methven, L., Wagstaff, C. (2023). Transcriptomic Differences Between Cultivation Locations Cause Significant Changes in Sulfur, Glucosinolate, Volatile Organic Chemical and Sugar Compositions of Eruca vesicaria subsp. sativa. In prep. Contact: luke.bell@reading.ac.uk 2. TERMS OF USE ------------ Copyright 2023 University of Reading. This dataset is licensed under a Creative Commons Attribution 4.0 International Licence: https://creativecommons.org/licenses/by/4.0/.[SD3] 3. PROJECT AND FUNDING INFORMATION ------------ Title: Smart breeding for salad rocket Dates: Sep 16 - Sep 20 Funding organisation: BBSRC, Elsoms Seeds Ltd., Bakkavor Ltd. Grant no.: BB/N01894X/1 4. CONTENTS ------------ File listing Eruca vesicaria RNAseq gene expression data.xls - Column A: Gene id - Columns B-DR: sample gene expression values (fpkm) - Column DS: Gene name - Column DT: Reference genome scaffold number - Column DU: Gene start position on scaffold - Column DV: Gene end position on scaffold - Column DW: DNA strand orientation (+/-) - Column DX: Gene length (in base pairs) - Column DY: (redundant) - Column DZ: Genome annotation description - Column EA: Gene family 5. METHODS ----------- RNA extraction, sequencing, bioinformatics and co-expression analysis were performed according to the methods described by Bell et al. (2020). All samples were checked for degradation and contamination by gel electrophoresis, Qubit fluorometer, NanoDrop (Thermo Fisher Scientific, Loughborough, UK) and Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). Samples not meeting all quality criteria were omitted from downstream analyses (UK trial, lines 21, 25, and 68; 2nd cut D5). RNA library preparation, sequencing, and bioinformatics were performed by Novogene Ltd. (Cambridge, UK) as a service.