Outsourcing of consultancy services w.r.t. Whole Transcriptome (Total RNA) Sequencing of Parkinson disease (PD), Healthy Control and Phytoextract treated Samples.

Scope of Work: Whole Transcriptome (Total RNA) Sequencing of Parkinson’s disease (PD), Healthy Control and Phytoextract treated Samples 1. Sample Receipt & Documentation a. Receive and log total RNA samples from PD animal model and healthy controls. b. Store RNA under appropriate conditions to maintain integrity. 2. RNA Quality Control a. Assess RNA quantity and purity (Gel, Nanodrop and Bioanalyzer). b. Check RNA integrity (RIN). 3. Library Preparation a. Ribodepletion to remove rRNA and enrich for coding and non-coding RNA. b. Construction of stranded total RNA libraries using validated kits. 4. Library QC & Quantification a. Validate library size distribution (Bioanalyzer and Qubit). b. Quantify libraries using Qubit and qPCR for accurate pooling. 5. Next-Generation Sequencing a. Sequence libraries on Illumina NovaSeq 6000 S4 reagent kitV1.5 b. Paired-end 2 x 150 bp reads. c. Target output: ~ 30-40 million reads (~9 GB data) per sample. 6. Bioinformatics Analysis • QC and trimming • Mapping to the reference genome • Quantification using feature counts • Differential expression analysis (either gene/transcript) • Gene Ontology analysis • Pathway analysis using KEGG database • Comparing with other data present in the different databases/datasets • Co-regulatory network analysis and network map construction • Heat Maps, Volcano plot, Venn diagram, PCA Plot, Dot Plots • NCBI Submission 7. Data Delivery & Reporting a. Provide raw sequencing data (FASTQ files). b. Processed expression matrices and analysis results. c. Comprehensive report summarizing methods, QC, and findings. Expected outcome: Differential gene expression, co-regulatory network analysis and network map construction in Parkinson’s disease, Healthy Control and Phytoextract treated Samples

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