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 translatome analysis (ribosome profiling) of 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 through 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 RNA-seq to RIBO-seq data allows to measure “translation efficiency”, i.e., rate of translation per mRNA unit.

High-Throughput Sequencing

We have partnered with 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.

Besides quality-control, gene expression and differential expression analyses, we perform 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 each client to understand their research questions and to ensure alignment in the 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 for the identification of alternative translation-initiation sites, termination read-through, translation of peptides in UTR regions (uORFs and dORFs), and for the discovery of translated ORFs in non-coding RNAs.

Differential Gene Expression

We utilize the most robust statistical tools for assessing differential gene expression between conditions, including the EdgeR software package (Lun et al. 2016) for statistical analysis of differential transcription and translation, and the anota2seq package (Oertlin et al. 2019) for statistical analysis of differential Translation Efficiency and Buffering.

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 Translation Patterns

With RIBO-seq we can identify changes in translation efficiency along coding regions. To this purpose we developed computational pipelines to identify sequence positions subject to translational pausing and codon types with differential Relative Codon Occupancy (Nedialkova and Leidel 2015), and to test for 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.