{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Mark Sterken"],"organism":["Globodera pallida"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15408"],"description":["We aimed to identify loci under selection for virulence in the potato cyst nematode Globodera pallida. Therefore, two G. pallida populations with suspected virulence, designated AMPOP02 and AMPOP10, were used in a selection experiment on the resistant potato variety Seresta. The selection experiment started in 2015, going through one generation per year, leading to fourth-generation selection populations at the end of 2018. The experiment was conducted in large pots, with a population that was as large as possible. After each generation cysts were saved for a later pot-experiment. This pot experiment was conducted in 2019 where the replication of these G. pallida populations on a set of potato cultivars (amongst others the non-resistant cultivar Desiree and the resistant cultivar Seresta). The first priority with the resulting generation was quantification and thereafter the material resulting from the Desiree and Seresta propagation was frozen in liquid nitrogen for DNA isolation. For each generation/potato cultivar combination three replicates were conducted. In total we had therefore 60 samples. Unfortunately, after DNA isolation, we had material of sufficient quantity and quality to conduct DNA sequencing on 45 samples."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - J2 larvae collected after counting were frozen and stored at -80°C. These were lysed  and DNA was isolated using phenol/chloroform/isoamyl alcohol. DNA quantities were determined using Qubit Fluorometer (Invitrogen). Because we were dependent on how well the material was preserved after counting not all samples provided DNA of sufficient quantity and/or quality, 45 out of 60 samples were successfully sequenced.","Sample Collection - A maximum of 10,000 eggs was inoculated into two litre pots containing a 2.2 kg mixture of silver sand, kaolin, hydro grains and nutrients. To each of the pots, a potato piece containing a single shoot was added. To obtain sufficient starting material, prior to the selection experiment, AMPOP02 was propagated on the susceptible variety Desiree for two consecutive generations, resulting in AMpop02D2. AMPOP10 was propagated on Desiree for one generation, resulting in AMpop02D1.  For each generation, we aimed to save cysts to later use for DNA extraction.","Sequencing - DNA was sequenced using the BGISEQ-500 platform using the vendors standard protocols.","Library Construction - The DNA was sequenced at BGI Genomics (Hong Kong) using BGISEQ-500 with a median output of 295.4*106 reads of 100 bases (paired) per sample. Upon arrival the samples, integrity and purity were tested by gel-electrophoresis. Per sample 1 µg of DNA was fragmented by Covaris and fragments in the size ranges of 150-250 bp were selected which were subsequently quantified by Qubit. Fragments were end-repaired and 3’ adenylated prior to adaptor-ligation to the 3’ end. The fragments were amplified by PCR and purified with the Agencourt AMPure XP-Medium kit. DNA was quantified by Agilent 4200 TapeStation. Double stranded PCR products were circularized, and the circular DNA was used as input for sequencing in the BGISEQ-500 platform."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The variants were mapped to the G. pallida Rookmaker reference genome using bwa_mem2 and variants were called using bcftools. Next, variants were filtered for quality, coverage and, being a SNP. The remaining variants were converted to an alternative allele frequency where 0 is equal to the reference sequence and 1 is a fixed alternative allele. Note that these samples are derived from populations of thousands of individuals."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["BGISEQ-500"],"study_type":["DNA-seq"],"species":["Globodera pallida"],"pubmed_authors":["Stefan van de Ruitenbeek","Mark Sterken","Geert Smant"],"additional_accession":[]},"is_claimable":false,"name":"DNAseq of five generations of a selection experiment on two populations of Globodera pallida","description":"We aimed to identify loci under selection for virulence in the potato cyst nematode Globodera pallida. Therefore, two G. pallida populations with suspected virulence, designated AMPOP02 and AMPOP10, were used in a selection experiment on the resistant potato variety Seresta. The selection experiment started in 2015, going through one generation per year, leading to fourth-generation selection populations at the end of 2018. The experiment was conducted in large pots, with a population that was as large as possible. After each generation cysts were saved for a later pot-experiment. This pot experiment was conducted in 2019 where the replication of these G. pallida populations on a set of potato cultivars (amongst others the non-resistant cultivar Desiree and the resistant cultivar Seresta). The first priority with the resulting generation was quantification and thereafter the material resulting from the Desiree and Seresta propagation was frozen in liquid nitrogen for DNA isolation. For each generation/potato cultivar combination three replicates were conducted. In total we had therefore 60 samples. Unfortunately, after DNA isolation, we had material of sufficient quantity and quality to conduct DNA sequencing on 45 samples.","dates":{"release":"2025-08-05T00:00:00Z","modification":"2025-08-04T07:18:40.302Z","creation":"2025-07-29T12:17:41.51Z"},"accession":"E-MTAB-15408","cross_references":{"ENA":["ERP177379"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002693","EFO_0005518","EFO_0003816","EFO_0004184"]}}