{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Katie Stevens"],"organism":["Solanum tuberosum"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16611"],"description":["The experiment aimed to determine if potato and P infestans effectively process exogenous dsRNA. Both whole potato plants and in vitro P infestans were treated with 10 µg of dsRNA. Total RNA was extracted with the mirVana™ miRNA Isolation Kit. Library preparation and sequencing was conducted by NGI Sweden, SciLifeLab using a NovaSeq 6000 SP-100 flowcell. sRNA sequencing analysis demonstrated that both plant and pathogen effectively process target dsRNA into sRNAs, producing distinct populations of sRNA."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was extracted with the mirVana miRNA isolation kit.","Sequencing - Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.8.1/RTA v3.4.4) with a 101nt(Read1)-8nt(Index1)-8nt(Index2) setup using 'NovaSeqStandard' workflow in 'SP' mode flowcell.","Sample Collection - For P infestans, following a 12 hour incubation of dsRNA samples were collected by flash freezing micro eppendorf tubes. For plant samples, 48 hours post dsRNA spraying leaf samples were selected and flash frozen.","Library Construction - Library preparation and sequencing was conducted by NGI Sweden, SciLifeLab using a NovaSeq 6000 SP-100 flowcell."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - fastp was used to remove adapter sequences and obtain reads 16-30 base per in length, duplicate reads were removed using umi tools [27, 28]. Reads were uniquely aligned to the PITG_06376 target gene using ShortStack (v 4.0.3) with default parameters [29]; normalised coverage of reads was calculated using Samtools [30]. For whole genome alignments, reads mapping to ribosomal RNA, transfer RNA and both the potato reference genome (https://spuddb.uga.edu/) and P. infestans genome (https://protists.ensembl.org/index.html) were removed before alignment and counting using Shortstack."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["microRNA profiling by high throughput sequencing"],"species":["Solanum tuberosum"],"pubmed_authors":["Katie Stevens"],"additional_accession":[]},"is_claimable":false,"name":"Spray-Induced Gene Silencing (SIGS) with dsRNA: Efficacy, stability, and processing in potato plant protection against Phytophthora infestans","description":"The experiment aimed to determine if potato and P infestans effectively process exogenous dsRNA. Both whole potato plants and in vitro P infestans were treated with 10 µg of dsRNA. Total RNA was extracted with the mirVana™ miRNA Isolation Kit. Library preparation and sequencing was conducted by NGI Sweden, SciLifeLab using a NovaSeq 6000 SP-100 flowcell. sRNA sequencing analysis demonstrated that both plant and pathogen effectively process target dsRNA into sRNAs, producing distinct populations of sRNA.","dates":{"release":"2026-03-31T00:00:00Z","modification":"2026-03-31T07:47:54.044Z","creation":"2026-02-09T13:24:37.524Z"},"accession":"E-MTAB-16611","cross_references":{"ENA":["ERP188889"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002896","EFO_0005518","EFO_0003816","EFO_0004184"]}}