biostudies-arrayexpressMark SterkenGlobodera pallidahttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15069We explored the sex determination of Globodera pallida. To do so, we grew cuttings of the potato cultivar Desiree on Gamborg B5 medium supplemented with either 1.5 g/L or 20 g/L sucrose. 14-day-old cuttings were inoculated with 100 G. pallida E400 Rookmaker juveniles. Infected root tissue was harvested at 1, 3, 6, and 9 dpi. Also, a subsample of the ppJ2 was kept for each batch. The experiment contains four time-separated batches. Small RNA sequencing was performed by BGI Hong Kong.biostudies-arrayexpressLibrary Construction - Small RNA samples were pre-treated with RNA 5’ Polyphosphatase (Biosearch™ Technologies, UK). And ≥1ug of total RNA was send for sRNA sequencing to BGI Genomics (Hong Kong, China).Nucleic Acid Extraction - Total RNA was extracted with the Maxwell 16 LEV-plant RNA kit (Promega, USA), according to the manufacturer’s instructions.Sequencing - For small RNA sequencing stranded libraries were sequenced on the DNBseq platform, generating over 20 million single-end 50 base pair reads per sample.Sample Collection - In vitro infection assays were performed as described by Goverse et al. (2000) with additions made by Zheng et al. (2022). In brief, we used cuttings of the susceptible potato cultivar Desirée, which were grown on Gamborg B5 medium supplemented with either 20 g/L or 1.5 g/L of sucrose. After 14 days, cuttings were inoculated with 100 G. pallida Rookmaker J2s per plate. We harvested infected roots at 1, 3, 6, and 9 days post inoculation (dpi). At 1 and 3 dpi, infected root segments of 15 plants were pooled per sample and at 6 and 9 dpi, infected root segments of 10 plants were pooled per sample.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Small RNA reads were processed using ShortStack (v4.0.3). First, trimmed reads of the pre-parasitic samples were merged and mapped against the G. pallida Rookmaker genome (PRJEB91928) to generate a structural annotation. Resulting BAM files were loaded into SeqMonk , from which reads per kilobase million (RPM) values were extracted.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsDNBSEQ-G400Maxwell 16 LEV-plant RNA kitRNA-seq of non coding RNAGlobodera pallidaStefan van de RuitenbeekArno SchavelingMark SterkenGeert SmantfalseSmall RNA-seq on a time series of potato infected with Globodera pallidaWe explored the sex determination of Globodera pallida. To do so, we grew cuttings of the potato cultivar Desiree on Gamborg B5 medium supplemented with either 1.5 g/L or 20 g/L sucrose. 14-day-old cuttings were inoculated with 100 G. pallida E400 Rookmaker juveniles. Infected root tissue was harvested at 1, 3, 6, and 9 dpi. Also, a subsample of the ppJ2 was kept for each batch. The experiment contains four time-separated batches. Small RNA sequencing was performed by BGI Hong Kong.2025-11-05T00:00:00Z2025-11-05T11:22:11.679Z2025-04-23T13:16:59.187ZE-MTAB-15069ERP180437EFO_0003737EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0004184