We provide

cost effective experimental design and execution of functional genomics projects based on the RIBO-seq platform.

TB-Seq specializes in application and development of experimental and computational procedures for identification and analysis of ribosome-protected mRNA footprints (ribosome profiling), from mammalian cell lines and tissues, plants, fungi, bacterial cultures, and metagenome communities.

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Let’s work on your project together

Experimental Design

Since 2015, TB-Seq has provided to its international customers from academia, biotech and pharma the highest quality experimental and computational products in ribosome profiling (RIBO-seq) analysis. We offer competitive pricing, fast turn-around, highest quality of execution, and customized project and experimental design and execution, to fit your needs from data collection, through data analysis, to result summary.

TB-Seq Inc. labs are located in South San Francisco CA, at the core of the San Francisco peninsula Biotech hub and in close proximity to Stanford University and UCSF.

We will be glad to discuss with you your project details.

  • Our team has combined decades of experience in scientific research and can assist you in creating a robust and effective experimental design.

  • We will discuss with you the most appropriate experimental strategy and applications of ribosome-profiling techniques in relation to your samples, your scientific/development goals, and your budget.

  • We are specialized in projects focused in functional genomics analysis utilizing the RIBO-seq platform.

RIBO-seq library preparation

We are experienced in isolating ribosome-bound mRNA from bacterial and eukaryotic cells, and from animal and plant tissues. We have developed sample-specific efficient protocols for all steps of the RIBO-seq procedure, from lysis to library preparation, that allow us to create RIBO-seq libraries of the highest quality from the smallest amount of starting material.

Our proprietary optimized RIBO-seq protocols allow us to produce RIBO-seq libraries of the highest quality more efficiently and with enhanced sensitivity compared to competing protocols.

Sample requirements

  • You provide your frozen cell or tissue samples, and TB-Seq carries out the entire RIBO-seq library preparation, including cell lysis, monosome isolation and purification, rRNA depletion, gel-isolation of ribosome-bound RNA fragments, cDNA synthesis from the isolated RNA and library prep. for Illumina sequencing.

  • We offer sequencing services through a third party or we deliver the library to you for sequencing by your favorite provider.

  • Turn around time is usually 3-4 weeks for library preparation and one week for sequencing.

RNA-seq libraries

We will be glad to prepare RNA-seq libraries in parallel to RIBO-seq libraries upon request. Comparing RIBO-seq to RNA-seq coverages allows to normalize ribosome coverage by transcript coverage.

High-Throughput Sequencing

We have partnered with experienced sequencing facilities that guarantee fast sequencing services on Illumina HiSeq or NovaSeq sequencers.

Bioinformatics analysis of NGS data

TB-Seq offers a wide range of bioinformatics analyses based on RIBO-seq and RNA-seq sequencing data, ranging from basic quality-control and gene coverage analysis, to differential gene coverage analysis, ORF analysis of 3-periodicity in coverage, codon occupancy analysis, and more.

TB-Seq offers customized analyses tailored to your research needs, using available software packages, our suite of bioinformatics tools, or developing ad hoc analytical tools.

Our team works side-by-side with all clients to understand their research questions and to ensure alignment to their study objectives.

Read Preprocessing

Our preprocessing pipeline allows precise quality control and 3’-adapter and poly-A sequence trimming for maximal data-integrity preservation.

Read Alignment

We use the fastest and most accurate algorithms to align reads to your favorite reference sequences (genomic or otherwise). We perform QC analysis of consistency in gene coverage between replicates, analysis of congruency between RIBO-seq and RNA-seq gene coverages, and analysis of footprint length distribution.

New Protein/Peptide and Alternative Translation Initiation Site identification

We have developed proprietary tools for statistical analysis of RIBO-seq coverage patterns that help the identification of alternative translation-initiation sites, termination read-through, translation of peptides in UTR regions (uORFs and dORFs), and in the discovery of translated ORFs in non-coding RNAs.

Differential Gene Coverage

We utilize the most robust statistical tools for assessing differential gene coverage between conditions, including the EdgeR software package (Lun et al. 2016) for statistical analysis of differential RNA-seq and RIBO coverages, and the anota2seq package (Oertlin et al. 2019) for statistical analysis of differential RIBO-seq coverage normalized by RNA-seq coverage.

Pathway and Motif Enrichment Analysis

We perform functional-enrichment statistical analysis for significant terms from KEGG Pathways, Gene Ontology (Biological Processes, Molecular Function and Cellular Component), and Reactome Pathways knowledge bases with reString (Manzini et al. 2021). We identify enrichment of new and known sequence motifs with HOMER v3.0 (Heinz et al. 2010).

Gene Coverage Patterns

With RIBO-seq we can identify changes in codon occupancy along coding regions. To this purpose we developed computational pipelines to identify sequence positions enriched in stalled or inactive ribosome, codon types with differential Relative Codon Occupancy (Nedialkova and Leidel 2015), and differences in Cumulative Coverage along the sequence (Shalgi et al. 2013).

All information on our ribosome profiling services is subject to change without notice. Please contact TB-SEQ Inc. for latest pricing and terms.