{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jinzhuo Jian"],"organism":["Triticum aestivum"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15943"],"description":["The mapped reads of each sample were assembled using StringTie (v2.2.3) (Pertea et al., 2015) in a reference-based approach. Read counts mapped to each gene were quantified using FeatureCounts (v2.0.6). Differential gene expression analysis was performed with the DESeq2 R package (1.42.0), applying the following significance thresholds: padj ≤ 0.05 and |log2(fold change) | ≥ 1. Raw read counts were normalized to transcripts per kilobase million (TPM) for gene expression quantification. For downstream analyses, read counts were averaged across three biological replicates. The resulting clusters were visualized with the RSEM software. Gene Ontology (GO) enrichment analysis was conducted using the clusterProfiler R package (v4.8.1). Additionally, clusterProfiler was employed to test the statistical enrichment of differentially expressed genes in KEGG pathways."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - The wheat cultivar Fielder was used for transgenic studies, plant-nematode interaction analyses, and parasitism assays.Both plant species were maintained in growth chambers under controlled conditions (23°C, 16-h light/8-h dark photoperiod).","Sequencing - First, cells are lysed with a detergent-based buffer to release their contents. The nucleic acids are then separated from contaminants by binding to a silica column, followed by washing and elution in a clean buffer to yield a pure sample.","Library Construction - First, fragmented DNA undergoes end repair and A-tailing to create compatible ends. Then, sequencing adapters are ligated to the fragments, followed by purification and PCR amplification to generate the final library.","Sample Treatment - First, collect cyst nematodes (Heterodera avenae) from an infested field in Qingdao, China. Then, inoculate wild-type and overexpression wheat roots with these nematodes, while maintaining a non-inoculated set of plants as a negative control. Finally, collect all root samples three days after inoculation.","Nucleic Acid Extraction - Total RNA was extracted using TRIzol reagent (Invitrogen, catalogue number 15596018). First-strand cDNA was synthesized from 1 μg of total RNA using the PrimeScriptTM RT reagent Kit with gDNA Eraser (Takara).","Sample Collection - Cereal cyst nematode H. avenae (Treub) Chitwood were collected from an infested wheat field in Qingdao, China. The roots of Wild type and overexpressed wheat were inoculated with Ha nematodes, and the roots were collected 3 days later, with no inoculation as a negative control."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - First, read counts are normalized using a method such as TPM or DESeq2 to account for library size and gene length. The normalized data is then often log2-transformed to stabilize variance and improve performance for downstream statistical analysis."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Triticum aestivum"],"pubmed_authors":["Jinzhuo Jian"],"additional_accession":[]},"is_claimable":false,"name":"Manipulation of Vacuole-Mediated Redox Homeostasis by Cyst Nematode Effectors Promotes Feeding Site Formation and Parasitism","description":"The mapped reads of each sample were assembled using StringTie (v2.2.3) (Pertea et al., 2015) in a reference-based approach. Read counts mapped to each gene were quantified using FeatureCounts (v2.0.6). Differential gene expression analysis was performed with the DESeq2 R package (1.42.0), applying the following significance thresholds: padj ≤ 0.05 and |log2(fold change) | ≥ 1. Raw read counts were normalized to transcripts per kilobase million (TPM) for gene expression quantification. For downstream analyses, read counts were averaged across three biological replicates. The resulting clusters were visualized with the RSEM software. Gene Ontology (GO) enrichment analysis was conducted using the clusterProfiler R package (v4.8.1). Additionally, clusterProfiler was employed to test the statistical enrichment of differentially expressed genes in KEGG pathways.","dates":{"release":"2025-11-25T00:00:00Z","modification":"2026-05-27T16:48:22.757Z","creation":"2025-10-31T12:39:57.767Z"},"accession":"E-MTAB-15943","cross_references":{"ENA":["ERP183461"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}