biostudies-arrayexpressMark SterkenSolanum tuberosumhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15312In this experiment we follow the infection of potato by Globodera pallida populations AMPOP02 and Rookmaker. The goal of the experiment was twofold: (i) to follow the expression of effectors in the nematode, (ii) to follow the transcriptional response of the potato plant. In this experiment, we inoculated 14 day old potato cuttings of the variety Seresta with AMPOP02, Rookmaker, or a mock-infection. Root tissue was harvested at 1, 3, 6 and 9 days post infection. Also, a subsample of the pre-parasitic juveniles used as the inoculum was kept for each batch. The experiment contains four time-separated batches. RNA extraction was done in Wageningen. Sequencing was performed by BGI Hong Kong.biostudies-arrayexpressNucleic Acid Extraction - Total RNA was extracted with the Maxwell 16 LEV-plant RNA kit (Promega, USA), according to the manufacturer’s instructions.Library Construction - 1. Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; 2. mRNA molecules were fragmented into small pieces; 3. The fragmented mRNA was synthesized into first strand cDNA using random primers; 4. The second strand cDNA was synthesized with dUTP instead of dTTP; 5. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 6. Perform PCR amplification; 7. Library quality control; 8. Library circularization; 9. The library was amplified to make DNA nanoball (DNB); 10. Sequencing on DNBSEQ (DNBSEQ Technology) platform.Sample Collection - To assess the transcriptome of pre-parasitic and parasitic G. pallida juveniles in vitro infection assays were performed as described before (Zheng et al., 2022). In brief, Rookmaker and AMpop02DS4 cysts were hatched according to Goverse et al. (2000). Pre-parasitic second stage juveniles (ppJ2s) were collected, cleaned by sucrose purification (Jenkins, 1964) and surface-sterilized in 0.008% (w/v) mercuric chloride. Fourteen-day-old stem cuttings of the potato cultivar Seresta, were inoculated with 100 surface-sterilized Rookmaker or AMPOP02 ppJ2s. After inoculation, plants were kept in the dark at 18 °C, and infected root segments were harvested 1-, 3-, 6-, and 9-days post inoculation (dpi). Each sample consisted of the infected root tissue pulled from 10 plants. At each batch, a subsample of the inoculum was used to assess transcription in ppJ2s. Four independent hatchings were used to conduct four time-separated biological replicates of the experiment.Sequencing - Stranded libraries were sequenced on the DNBseq platform, generating an average of 77.7 million paired-end 150 base pair read pairs per sample.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Reads were mapped to both the G. pallida Rookmaker reference genome (PRJNA1268174) as well as the potato reference genome DM 1-3 (v6.1). This was done using hisat2 and counted using mosdepth. Samtools was used to sort and organize the mapped reads. Counts were TPM normalized for further analysis.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsDNBSEQ-G400Maxwell 16 LEV-plant RNA kitRNA-seq of coding RNASolanum tuberosumStefan van de RuitenbeekArno SchavelingMark SterkenfalseTime-series RNA-seq on potato root tissue infected by two populations of Globodera pallidaIn this experiment we follow the infection of potato by Globodera pallida populations AMPOP02 and Rookmaker. The goal of the experiment was twofold: (i) to follow the expression of effectors in the nematode, (ii) to follow the transcriptional response of the potato plant. In this experiment, we inoculated 14 day old potato cuttings of the variety Seresta with AMPOP02, Rookmaker, or a mock-infection. Root tissue was harvested at 1, 3, 6 and 9 days post infection. Also, a subsample of the pre-parasitic juveniles used as the inoculum was kept for each batch. The experiment contains four time-separated batches. RNA extraction was done in Wageningen. Sequencing was performed by BGI Hong Kong.2025-08-05T00:00:00Z2025-08-04T07:18:09.002Z2025-08-01T11:22:54.075ZE-MTAB-15312ERP177699EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184