​​​​​​​Ribosome Profiling Services

​​​​​​​TB-SEQ, Inc. is a life-science company devoted to the development and application of experimental and computational procedures for functional (meta)genomics analysis of prokaryotic and eukaryotic organisms and communities based on the ribosome profiling NGS platform technology (RIBO-seq) and on computational analysis of sequencing data. TB-Seq develops new experimental protocols and bioinformatics tools applicable to different biological system, and offers ribosome profiling (RIBO-seq) and RNA-seq related services. Our team combines decades of experience in research and development in computational sequence analysis, molecular biology and biochemistry, in experimental analysis of nucleic acids, and in protein and nucleic acid sequence and structure computational analysis.

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

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 and high-quality pictures for publication purposes.

Experimental Design
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.

We provide cost effective consultation on experimental design for functional genomics projects based on the RIBO-seq platform. We will be glad to discuss with you your project details.

 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. Upon request we provide standard and customized bioinformatics analysis.  We perform standard bioinformatics analysis (mapping of RIBO-seq reads to genome sequence and library-quality assessment based on meta-gene 3-base periodicity and rRNA contamination assessment) (one week turn-around). We will be happy to discuss with you customized bioinformatics and statistical analyses.

Please inquire for a quote with the form below.

 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

Read Preprocessing
Our preprocessing pipeline allows precise quality control and 3'-adaptor and poly-A sequence trimming for maximal data-integrity preservation.

 Read Alignment
We use the fastest alignment algorithms to characterize perfect, approximate, unique, multiple and discarded read alignment. We work with you to align reads to your favorite reference sequence (genomic or otherwise). We perform ribosome footprint to RNA-seq read alignments for congruency analysis.

New Protein/Peptide and Alternative Translation Initiation Site identification
We have developed proprietary computational tools for the effective identification, analysis, and graphical representation of patterns of protein translation of potential interest, including differential translation, use of alternative TIS, uORF, and AltORF identification.

Differential Gene Expression
We utilize the latest statistical tools for assessing differences in gene expression (RNA-sequencing data) and protein expression (RIBO-sequencing data) across conditions accounting for over-dispersion of sequencing data, including PERMANOVA analysis, negative-binomial fitting, Log-normal fitting and Bayesian inference, and sampling the distribution of the statistics from replicates of experimental samples. Summary data on gene and protein relative expression are provided.

Gene ontology and pathway analysis
Including GSEA gene set enrichment and Leading Edge analyses, Impact Analysis (ROntoTools) and iPathwayGuide.

Advanced services
We have the computational capabilities to perform customized analyses on your sequencing data, using available software packages, our suite of bioinformatics tools, or by developing new analytical tools according to your needs. Whatever the information you are looking to extract from your data, we will be happy to discuss with you the most appropriate computational-analysis design, and to execute it for you.

Our team works side-by-side with each client to understand their research questions and to ensure alignment in the study objectives.

 For a quote on our services please fill out the form below or visit us on ScienceExchange.

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