Transcriptome & Genotypage platform

The regional “Transcriptome & Genotyping” core facility, located at the Institute for Regenerative Medicine and Biotherapy (IRMB) of the Montpellier University Hospital (Saint-Eloi Hospital), is part of the Montpellier GenomiX (MGX) network, which brings together the genomics platforms in the Montpellier area. Open to the entire academic, clinical, and industrial scientific community, our platform offers cutting-edge services in areas such as high-throughput sequencing (Illumina NGS), single-cell RNA-seq analysis (10X Genomics, Fluidigm), and DNA microarray hybridization (Affymetrix, for both cytogenetics and gene expression profiling). Specializing in genome and transcriptome analysis, we provide access to the latest technologies, including high-throughput PCR (Fluidigm). Thanks to its location at the heart of the Montpellier University Hospital, the platform benefits from unique expertise in applying sequencing and microarray technologies to medical research. It is notably involved in major projects such as Immuno4Cure, a flagship initiative of the University Hospital Institute (IHU) dedicated to autoimmune diseases. We have also developed specific expertise in transcriptome analysis from extremely low quantities of RNA, including human oocyte pools and cell subpopulations sorted by flow cytometry. 

The platform is open to all users, whether from public institutions or the private sector. Numerous research teams from France and across Europe have already relied on our expertise for their bulk RNA-seq, single-cell RNA-seq, or DNA microarray projects.

Services offered by the platform

Automated nucleic acid extraction

RNA / DNA Extraction Preparation: We offer RNA and DNA extraction services using advanced automated systems capable of processing a wide variety of sample types (cells, tissues, biological fluids) while ensuring the preservation of nucleic acid integrity and quality. Automation minimizes the risk of cross-contamination, improves reproducibility, and increases processing efficiency. This service option can be provided to research teams that are unable to perform the extraction themselves and must be discussed in advance with the platform managers.

The service includes:

• RNA Extraction: We provide high-quality RNA extracts free from contaminants, ready for applications such as RNA-Seq, real-time PCR, or gene expression analysis.
• DNA Extraction: We prepare high-purity DNA extracts suitable for genotyping, PCR, and sequencing applications. We use optimized protocols to maximize yield while minimizing the presence of inhibitors that could interfere with downstream analyses.

Nucleic acid quality control service

Our platform offers a comprehensive nucleic acid (RNA/DNA) quality control service, essential for ensuring the reliability of downstream analyses such as sequencing or PCR. This quality control is based on high-precision instruments that allow detailed assessment of the purity, integrity, and concentration of samples. We use a combination of tools to ensure optimal results, regardless of the sample type being analyzed.

Service Details:

• Qualification of nucleic acid extracts:
  Quality control of nucleic acids is performed through a series of tests to assess:

• Purity: Measurement of the A260/A280 ratio for RNA/DNA to evaluate contamination by proteins or other organic compounds.
• Integrity: Verification of the size and integrity of RNA or DNA fragments, which is crucial for applications such as RNA-Seq or genotyping. Excessive degradation or fragmentation can compromise analysis results.
• Concentration: Measurement of RNA or DNA concentration in the sample to ensure it is sufficient for downstream analyses.

The integration of multiple technologies (Nanodrop, Qubit, Bioanalyzer, Qsep1) ensures a complete and thorough quality control process, which is essential before proceeding to the next stages of your research projects.

RNA sequencing (RNA-Seq) service :

RNA sequencing (RNA-Seq) is a powerful approach for identifying and quantifying mRNA transcripts, providing essential insights into biological systems. Through RNA-Seq, we can uncover critical information such as:

• Cellular responses to treatments or disease conditions.
• Differential gene expression between experimental groups or states.

Our RNA-Seq service is performed using the Illumina NextSeq 550 platform, ensuring high-quality, high-throughput sequencing data tailored to your research needs. We provide comprehensive support to facilitate precise and reliable transcriptome profiling.

We offer a full range of services, including:

• Strand-specific sequencing of polyadenylated RNA (coding strand).
• Non-strand-specific sequencing of polyadenylated RNA.
• Small RNA sequencing: miRNA, siRNA, etc.
• Strand-specific sequencing of non-polyadenylated RNA (depletion).
• Sequencing of very low RNA quantities (starting from 1 ng of RNA).

Our expertise and technology allow us to tailor each analysis to meet the specific requirements of your projects while ensuring reliable and detailed results.

Single cell RNA sequencing (scRNAseq) service:

Single-cell RNA sequencing enables transcriptome analysis at the resolution of individual cells, providing a powerful approach to unravel cellular heterogeneity within complex biological samples. This technique is essential for dissecting the diversity of cellular states, understanding differentiation dynamics, and exploring the molecular mechanisms underlying physiological and pathological processes.

Our platform offers several complementary technologies to meet a variety of research needs:

• 10x Genomics Chromium technology: The 10x Genomics Chromium platform enables high-throughput single-cell analysis by encapsulating thousands of individual cells into microdroplets (GEMs) for parallel transcriptome capture and profiling. It is particularly well-suited for studies requiring large cell numbers and broad coverage of cellular subpopulations. We also offer specialized applications using this technology, including BCR (B-cell receptor) and TCR (T-cell receptor) analyses, allowing for detailed exploration of antigen receptor repertoires and deeper insights into immune responses.
• Fluidigm C1 and Biomark systems:
  • The C1 system enables the automated isolation and processing of single cells on dedicated microfluidic chips, with downstream mRNA amplification for detailed transcriptomic analysis. It is ideal for projects requiring precise control over cell capture (by size or type) and in-depth characterization at the single-cell level.
  • The Biomark system provides highly sensitive gene expression quantification using real-time PCR (qPCR) at the single-cell level, allowing targeted analysis of specific gene panels with great precision and cost-efficiency.

By combining these technologies, our platform supports a wide range of single-cell transcriptomics projects, from comprehensive transcriptome profiling to targeted gene expression studies.

Single nucleus RNA sequencing (snRNA-Seq) service :

• The majority of messenger RNA in a cell is typically found in the cytosol, while newly expressed transcripts are primarily located in the nucleus. When using intact, viable cells, gene expression is measured from the mRNA of the entire cell. However, when working with frozen tissue, isolating intact nuclei is simpler than recovering whole cells. For these samples, we offer the Single-Nucleus RNA-Seq (snRNA-Seq) approach, utilizing 10X Genomics technology, which allows for precise transcriptome analysis at the nuclear level, providing an optimal solution for frozen tissue samples.

Affymetrix Microarrays – Cytogenetics

• Cytogenetic analyses are performed to detect aneuploidies, microdeletions, microduplications, and other chromosomal abnormalities. Our platform offers the Applied Biosystems (formerly Affymetrix) microarray technology, providing a comprehensive genome-wide approach for the identification of chromosomal copy number variations and allelic imbalances. This reliable and sensitive system enables the study and characterization of copy number gains and losses, absence of heterozygosity (AOH), copy-neutral loss of heterozygosity (cnLOH), uniparental disomy, regions identical by descent, and mosaicism.
  • The CytoScan HD Accel assay workflow can be completed in just 2 days.
  • The assay input amount is 100 ng of genomic DNA,
  • The CytoScan HD Accel assay generates consistent target that is hybridized to the CytoScan HD Accel Array to yield reproducible and reliable results.
  • 2.8 millions markers for copy number analysis, including 750,000 SNPs and 2 millions nonpolymorphic probes
  • An intuitive software solution for cytogenetics and copy number analysis, enabling straightforward data processing and the creation of customized exports tailored to your specific needs.

Affymetrix Microarrays – microRNAs and Gene expression profile

• Our platform offers specialized microRNA analysis using Affymetrix miRNA 4.0 arrays. This service provides comprehensive profiling of microRNA expression across a wide range of samples, offering detailed insights into the regulation of gene expression and the role of microRNAs in various biological processes.
• Our transcriptome platform provides high-precision gene expression analysis using Affymetrix arrays such as Clarion D, Ewon ST, HTA 2.0 A, U133, and more. These arrays offer extensive genomic coverage and exceptional sensitivity, enabling precise quantification of gene expression across diverse sample types. They are ideal for in-depth studies of gene regulation and biomarker discovery, ensuring reliable and reproducible results for advanced research projects.
• Single amplification from 100ng total RNA & Hybridization
• Double amplification from 10ng total RNA & Hybridization
• Amplification of very small samples from 600pg total RNA or from a few cells & Hybridization (Arcturus or NuGen).