Transcriptomics study in rice under stress along with bioinformatics analysis

For undertaking transcriptomics study in rice under stress along with bioinformatics analysis

1. Sample details • Number of biological samples: 22. • Tissue samples will be provided by AAU, Jorhat • Each biological sample will be sequenced in triplicate (biological replicates) (Total libraries = 66) • Sample collection and transport will be done using appropriate procedure, in multiple batches if required by service provider (To be borne by the vendor). 2. RNA extraction and library preparation • Total RNA isolation using a standardized, vendor-validated protocol matching to globally accepting norms. • RNA quality requirements: • RIN ≥ 7.0 • OD 260/280 = 1.8–2.1 • rRNA depletion–based library preparation • Sequencing library specifications: • Platform: Illumina (or equivalent) • Read type: Paired-end • Read length: 2 × 50 bp • Minimum data output: ~20 GB per sample • Base quality: ≥ 97% bases ≥ Q30 3. Sequencing quality requirements • ≥ 90% reads mapped to reference genome • Duplication rate ≤ 20% • Adapter contamination ≤ 1% 4. Bioinformatics analysis (end-to-end, publication ready) • Primary analysis • Raw data delivery: FASTQ files • Quality control: FastQC + MultiQC • Adapter trimming and quality filtering • Alignment to reference genome (organism to be specified by institute) • Output: Aligned BAM files • Expression analysis • Gene-level quantification (raw counts + normalized values: TPM/FPKM) • Differential gene expression analysis: • Group-wise contrasts (to be defined by institute) • Log₂FC, p-value, adjusted p-value (FDR) • Outputs: • Differentially expressed gene lists (Up- and Down-regulated) • CSV/Excel format tables • Downstream analysis • PCA, hierarchical clustering, correlation plots anything more you need. • Volcano plots, MA plots, heatmaps • Functional annotation: • GO enrichment • KEGG / pathway analysis • Read coverage visualization files (BigWig) • Final deliverables • Complete analysis report: • PDF + interactive HTML • All scripts and pipeline details for reproducibility Note: Peak calling, motif discovery, and differential binding analysis are not applicable to standard RNA-sequencing and are not required under this scope.