biostudies-arrayexpressChao XiangOryza sativa Japonica Grouphttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15844Transcriptome profiling of roots from Oryza sativa ssp. japonica cv. Nipponbare and Nipponbare mutant in response to root-knot nematode (RKN, Meloidogyne graminicola) infection. The experiment aimed to identify differentially expressed genes during early nematode establishment. Roots were collected at three time points: 0 days (uninfected control), 3 days, and 7 days post-inoculation. Each condition had three biological replicates. Total RNA was extracted and rRNA-depleted prior to library construction and sequencing.biostudies-arrayexpressSequencing - The quality-checked libraries were sequenced on an Illumina NovaSeq 6000 platform using a paired-end 150 bp (PE150) strategy. The target sequencing depth for each sample was approximately 40 million reads.Sample Collection - Rice root samples were collected at the following time points: (1) Baseline control group at 14 days of growth; (2) 3 days post-inoculation (3 dpi) with root-knot nematode (Meloidogyne spp.); (3) 7 days post-inoculation (7 dpi). During collection, roots were swiftly excised, rinsed thoroughly with sterile deionized water to remove the growth medium, immediately flash-frozen in liquid nitrogen, and stored at -80°C until nucleic acid extraction.Nucleic Acid Extraction - Total RNA was extracted from approximately 100 mg of frozen root tissue using the [Please specify the kit, e.g., QIAGEN RNeasy Plant Mini Kit], strictly following the manufacturer's instructions. The extracted RNA concentration was measured using NanoDrop, and its integrity was checked using an Agilent 2100 Bioanalyzer. The RNA Integrity Number (RIN) for all submitted samples was greater than 8.0.Growth Protocol - Rice (Oryza sativa L. ssp. japonica cv. Nipponbare) seeds were surface-sterilized and grown hydroponically in a controlled greenhouse (28°C/25°C day/night temperature, 14-hour light/10-hour dark cycle). All experimental materials included wild-type (WT), Thill gene overexpression (OE), and knockout mutant (KO) lines.Library Construction - Strand-specific RNA-seq libraries were constructed using the [Please specify the kit, e.g., NEBNext Ultra II RNA Library Prep Kit for Illumina]. The brief procedure was as follows: starting with 1 μg of total RNA, mRNA was enriched using Oligo(dT) beads, followed by fragmentation, cDNA synthesis, end repair, A-tailing, adapter ligation with indexes, and finally PCR amplification. The final libraries were purified and size-selected using AMPure XP beads.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - FPKM (Fragments Per Kilobase per Million mapped fragments) is a normalization method for RNA-seq data, primarily used with paired-end sequencing. It measures gene expression by normalizing for both gene length and sequencing depth. The formula is:FPKM = F / ( L * T ) F = Number of fragments mapped to the gene L = Gene length in kilobases (length/1000) T = Total mapped fragments in millions (total/1,000,000)MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAOryza sativa Japonica GroupChao XiangfalseTranscriptome profiling of roots from Oryza sativa in response to root-knot nematode (RKN, Meloidogyne graminicola) infectionTranscriptome profiling of roots from Oryza sativa ssp. japonica cv. Nipponbare and Nipponbare mutant in response to root-knot nematode (RKN, Meloidogyne graminicola) infection. The experiment aimed to identify differentially expressed genes during early nematode establishment. Roots were collected at three time points: 0 days (uninfected control), 3 days, and 7 days post-inoculation. Each condition had three biological replicates. Total RNA was extracted and rRNA-depleted prior to library construction and sequencing.2026-05-29T00:00:00Z2026-05-29T01:00:50.641Z2025-10-23T20:53:35.108ZE-MTAB-15844ERP182851EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003816EFO_0003738EFO_0004184