Functional genomics

Services

The FGCF offers internal genome-wide mutation expression and analysis services to researchers at public institutes and private companies. We are located in room S1C14 of the ‘Cluster I’ building of the Barcelona Science Park. If you are interested in a custom solution that is not included below, please contact us at genomics@irbbarcelona.org. We look forward to hearing about your projects and working side by side with you to overcome any experimental challenges.

• Experimental Design and Advice: Discuss your project with us and receive information on sample requirements and recommendations for your experimental design. This appointment is optional but highly recommended.
  Quality control of extracted nucleic acids, libraries and cells: all your samples will be subjected to quality control before processing, thus guaranteeing the NGS libraries of the highest quality. We use Nanodrop, Qubit, Bioanalyzer, and Countess instruments to determine concentration, sample quality, and cell viability.
• Nucleic acid extraction and purification: Having supported thousands of different projects, we are aware of the many challenges associated with collecting high quality DNA and RNA samples. Our toolkit includes cost-effective and highly efficient methods for RNA extraction and cDNA amplification from 100 cells or even from a single oocyte.
• Single-cell transcriptomics and multiomics: In April 2021, our facility successfully deployed the full capabilities of a 10X Genomics cell. In this sense, we offer:
  Analysis of unicellular gene expression.
  Monocellular ATAC-seq. Monocellular mutioma (secRNA-seq + ATAC-simultaneous seq).
  Unicellular immune profile.
  Directed gene expression.
  The 10X Genomics Chromium controller can capture 100 to 10,000 cells per sample and process up to eight simultaneous samples. Before you launch your project, you can provide us with your unicellular suspensions. In just 10 minutes, you will get a cellular quality control that will inform you of your cell processing and / or tissue dissociation workflow. Our team will help you with all the necessary steps to improve the preparation of the sample, obtain a service budget and schedule an appointment for the presentation of the sample.
• Library Preparation for Illumina’s Next Generation Sequencing (NGS): We use fully validated and community-accepted procedures for library preparation, ensuring consistent and reliable results. However, whenever necessary, we will align our operating procedures with the specific needs of your project.
  Sequencing of mRNA, lncRNA, miRNA and sRNA (RNA-seq): the whole transcriptome profile using NGS technologies provides a complete reading of the abundance of transcripts, the diversity of isoforms, as well as the discovery of new transcripts and genes of fusion. Our experienced staff will assist you with sample requirements, workflows, and sequencing strategies to achieve your project goals.
  Whole Genome Sequencing (WGS): Sequencing the entire genome of an individual allows the identification of somatic or germinal DNA variants.
  ChIP-seq and RIP-seq: These approaches combine chromatin immunoprecipitation (ChIP) or RNA (RIP) with NGS to identify protein-DNA or protein-RNA binding sites throughout the genome. In recent years, the FGCF has supported dozens of ChIP-seq and RIP-seq projects. We will assist you with linking, extraction, and fragmentation procedures to ensure that the highest quality libraries are obtained.
  Hi-C: The FGCF has implemented a workflow for capturing and sequencing chromosomal conformation that allows researchers to map the spatial organization of genomic DNA within cell nuclei and identify conformational interactions between nonadjacent regions .
  ATAC-seq: in this case, the accessibility of chromatin throughout the genome is interrogated through the accessibility of transposase to discover the extent and identity of regions prone to interact with transcription factors in cancer and others pathologies.
  Targeted sequencing: While WGS experiments may be your preferred option, their costs can still be prohibitive. Oriented approaches focus performance, and therefore cost, on defined subsets of genomic regions, thus allowing greater sequencing depths for safe variant detection at lower prices.
• Amplicon sequencing: PCR amplification of specific regions of interest reduces the target genomic space. There are several methods available for a complete and accurate panel design, allowing you to multiplex hundreds or thousands of amplicons in a single reaction. Feel free to contact us for a custom design and budget.
• Target capture, or sequence capture and enrichment: This alternative strategy reduces sequenced genomic space by “capturing” regions of interest with custom biotinylated probes. Entire exome sequencing is the most widespread Target Capture application. Our staff has extensive experience designing probes for target capture and will be happy to assist you with your project.
• Pico Profiling: This technique, pioneered by the FGCF, facilitates the generation of large amounts of saturated cDNA from very small cell populations. Our team has experience isolating RNA and amplifying cDNA from as few as 40 cells classified as mouse tumor organoids (MTOs) or from a single oocyte.
• Microarrays: sample of results of the analysis of gene expression of the whole genome for a wide variety of experimental organisms using Genechip matrices.
• DNA methylation: Multiple loci analysis for DNA methylation is still performed in an experimental phase. For specific projects on DNA methylation, please contact us.
• qPCR: A QuantStudio 6 Pro is available for booking. Departures must start within the working hours of the facility.
  Clone Collections: The FGCF has nearly 200,000 clones for your reverse genetics needs, including:
  human and mouse shRNA: The complete list of shRNA clones is available in this zip file. Detailed information on TRC1 clones is available on the Sigma MISSION shRNA library website and at the Broad Institute-based RNAi Consortium (TRC).
• Human ORF clones: The list of ORF clones is available in this zip file. Sequences from most clones in this collection (v1.1 edition) can be retrieved from the Harvard Center for Cancer Systems Biology hORFeome v7.1 database.