RNA Informatics, Technologies, and Therapies Core (RITTC)

The RNA Informatics, Technologies, and Therapies Core (RITTC) provides end-to-end support for studies of RNA translation, tRNA charging, and direct RNA modification detection.

Our team provides support from experimental design through data delivery, including consultation, sample processing, sequencing, data analysis, and results review. Whether you are planning a new study or need specialized analysis of existing data, we work with investigators to generate high-quality, reproducible datasets and publication-ready results.

Services Offered:

A. Ribosome Profiling (Ribo-seq) — Full-service ribosome profiling including cell lysis, nuclease digestion, ribosome-protected fragment isolation, library preparation (including rRNA depletion), Illumina sequencing, and matched input RNA-seq. This service produces publication-ready data on translation dynamics across the transcriptome.

B. Nanopore tRNA Sequencing — tRNA isolation, chemical and enzymatic adapter ligation, and direct RNA sequencing on the Oxford Nanopore PromethION platform. This service enables detection of tRNA modifications, charging levels, and isodecoder abundance without PCR amplification bias.

C. Nanopore Direct mRNA Sequencing — Direct mRNA sequencing on the Oxford Nanopore PromethION platform for full-length transcript analysis, enabling detection of RNA modifications, poly(A) tail lengths, and isoform-level quantification without reverse transcription or PCR amplification.

D. Informatics - Baseline informatics analysis is included with purchase of any sequencing technique listed above or can be purchased in hourly increments for additional custom requests.

• Ribosome Profiling — Bioinformatics analysis of Ribo-seq data including read alignment, quality assessment, P-site assignment, differential translation analysis, and codon-level resolution of ribosome occupancy.
• Nanopore RNA-seq — Bioinformatics analysis of nanopore tRNA sequencing and direct RNA sequencing data including basecalling, alignment, modification detection, and quantification of RNA features across both assays.
• Spatial Transcriptomics - Bioinformatics analysis of spatial transcriptomics data including quality assessment, spatial mapping of gene expression, differential expression analysis, cell type deconvolution, identification of spatially regulated genes, and generation of publication-ready visualizations.
• Single-Cell RNA-seq - Bioinformatics analysis of single-cell RNA sequencing data including quality assessment, identification of cellular subpopulations, cell type annotation, differential expression analysis, pathway enrichment, trajectory analysis, and generation of publication-ready visualizations.
• Analyst Flex Time — Flexible bioinformatics consulting for custom RNA sequencing analysis beyond standard pipelines.

Project Workflow

Start a Project

All projects begin with an initial inquiry form and a 30-minute consultation. This allows us to review your experimental design, sample type, replicate structure, sequencing goals, and analysis needs before samples are submitted.

Contact Us

Contact e-mail: [email protected]

Director: Jay Hesselberth, PhD

Co-Director: Neel Mukherjee, PhD