• rMATs Legend (PDF)
• Differential Gene Expression Legend (PDF)

• Goals: Determine study goals (e.g., differential gene expression, splicing variants, miRNA discovery).
• Sample Collection and Preparation: Discuss tissue/cell types, treatment conditions, and biological replicates.

• RNA Quality and Quantity: Evaluate RNA integrity and purity.
• Library Preparation: Choose the right library type (e.g., Poly(A) Enrichment, Ribosomal Depletion).
• Sequencing Parameters: Define depth, read length, and single-end vs paired-end sequencing.
• Data Analysis Planning: Type of analysis required (DEG, alternative splicing, miRNAs, circRNAs) and specific Aligners (e.g., HISAT2, STAR), and differential expression analysis (e.g., DESeq2, edgeR) tools.
• Type of Downstream Analysis: DEG selection, functional enrichment (e.g., GO, KEGG), protein interaction networks, miRNA-target networks

• Coordinate Sample Submission with company of choice (Novagene, UF/Scripps)
• Troubleshooting problems with sequencing facility
• Transfer raw data to HPC for analysis

• Prioritized Gene Lists: Provide a ranked list of differentially expressed genes for identifying biologically significant findings.
• Volcano Plots: Visualize gene expression changes with volcano plots that highlight significant up- and down-regulated genes.
• UCSC Genome Browser Track Files: Integrate RNASeq results with UCSC Genome Browser for seamless genomic annotations and visualization.
• Enrichment Analysis Reports: Provide functional analysis with GO, KEGG, and Reactome pathways to contextualize the biological relevance of the data.
• Protein Interaction Networks (PIN): Use STRING analysis to model protein–protein interaction networks, illustrating meaningful biological interactions.

We are currently developing additional pipelines for multi-omics analyses (e.g., ChIPSeq, ATACSeq, GEO-Seq, CUT&RNA, NanoPore, and scRNA-seq, etc.), which will allow for comprehensive analysis across different types of datasets.

These services are in development and will require additional time for full integration. We assess the feasibility of specific types of analysis on a case-by-case basis.

We provide expert consultation to help you validate differentially expressed genes (DEG) identified in your analysis phase. Our services include:

• Assay Recommendations: Guidance on the proper assays to use for validating DEG data, including but not limited to RT-qPCR, RT-PCR, and Nuclear Run-On assays.
• Primer Design: Support with designing primers for your assays to ensure high specificity and efficiency.
• Protocols: Assistance with selecting or creating protocols tailored to your specific validation needs.
• Reagent Purchase: Advice on the best reagents to purchase for your assays, ensuring high-quality results.

Raw sequencing files are transferred from a source server to the COM Genomics FAU High performance Computing (HPC) account. Source server can be located within:

• Sequencing facility
• GEO NIH database or other public databases
• Investigator’s or institute server (or other storage)

Human specimens should be de-identified to meet Exempt Category 4 - Secondary Uses of Identifiable Private Information or Identifiable Biospecimens (45 CFR 46 104 (d)(4))

We provide comprehensive support for uploading results and sequencing files to online databases, ensuring compliance with publication standards. Our services include:

• Assist in data upload to repositories like GEO or others:
  • Raw data and analysis are uploaded to the GEO NCBI database for publication purposes and indefinite storage.
  • This is a step required for the publication of data in a peer-reviewed journal.
  • A link to the GEO submission sheet may be provided, or the file can be made available for direct download from our site.
• Assist in generating methods sections, figures, and providing publication-ready data for manuscripts

• HPC Storage Space: Charges will be applied for storage and usage above the allocated quota of 3TB.
  • Large datasets (raw data): Can be temporarily stored for up to 60 days. After that, they must be moved to paid data storage within the HPC (see FAU HPC storage cost policies) or the NCBI GEO database (free of charge)

• RNA Extraction & Quality Control: Charges will be applied based on the reagents and time used for RNA extraction, quality control, and shipping of samples to the sequencing facility of your choice.