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Core Facilities & Services

Functional Genomics

Research information

Background

The Functional Genomics Core Facility (FGCF) at the Institute for Research in Biomedicine (IRB Barcelona) provides comprehensive support for bulk and single-cell genomics and transcriptomics projects. Our facility supports the entire IRB Barcelona research community, but also other scientists and groups from academia and industry.

We provide tailored solutions for a wide range of projects, including those with limited amounts of sample or samples whose quality is compromised. We also offer 10X solutions to all researchers interested in studying single-cell transcriptomics and epigenomics. The FGCF can provide support for the following projects:

  • Bulk Transcriptomics (mRNA-seq, miRNA-seq, sRNA-seq, and lncRNA-seq)
  • Single-cell mRNA Sequencing and Multiomics using 10X Genomics
  • Whole-Genome Sequencing (WGS)
  • Chromatin Immunoprecipitation and Sequencing (ChIP-seq)
  • RNA Immunoprecipitation and Sequencing (RIP-seq)
  • High‐Throughput Chromosome Conformation Capture (Hi-C/3C-Seq)
  • Amplicon Sequencing and Targeted Capture
  • Genomic and Transcriptomic Profiling to complement drug target identification screens, validations and biomarker discovery
  • Hi-Resolution On- and Off-target Analysis of CRISPR Genome Edits
  • Functional Validation of Genome Edits with RNA-seq, scRNA-seq, ChIP-seq, qPCR, etc.

What you can expect from us:

  • A bi-directional dialogue focused on customised solutions.
  • Agile project management to ensure that your requirements are met and easily adapted to last-minute modifications.
  • Availability to deploy pilot experiments to obtain preliminary data, test hypotheses, or troubleshoot methodologies.
  • End-to-end solutions and streamlined communication with the Biostatistics/Bioinformatics Core Facility or with your appointed bioinformatician.
  • Transparent and comprehensive sample processing and quality control reports.
  • The lowest price for your full-scale project thanks to the institutional support provided by IRB Barcelona.

Selected publications

Alexandra Avgustinova, Carmelo Laudanna, Mónica Pascual-García, Quirze Rovira, Magdolna Djurec, Andres Castellanos, Uxue Urdiroz-Urricelqui, Domenica Marchese, Neus Prats, Alexandra Van Keymeulen, Holger Heyn, Juan M. Vaquerizas, Salvador Aznar Benitah
Cell Stem Cell
(7;28(10 )
1790 -
1804
(2021)
Ewa Ksiezopolska, Miquel Àngel Schikora-Tamarit, Reinhard Beyer, Juan Carlos Nunez-Rodriguez, Christoph Schüller, Toni Gabaldón
Current Biology
(31.23 )
5314 -
5326
(2021)
Pascual G, Domínguez D, Elosúa-Bayes M, Beckedorff F, Laudanna C, Bigas C, Douillet D, Greco C, Symeonidi A, Hernández I, Gil SR, Prats N, Bescós C, Shiekhattar R, Amit M, Heyn H, Shilatifard A, Benitah SA
Nature
(599 )
485 -
490
(2021)
Rosa Pascual, Judit Martín, Fernando Salvador, Oscar Reina, Veronica Chanes, Alba Millanes-Romero, Clara Suñer, Gonzalo Fernández-Miranda, Anna Bartomeu, Yi-Shuian Huang, Roger R Gomis, Raúl Méndez
Science Advances
6
(eaax3868 )
(2020)
Anna-Lena Van de Weyer, Freddy Monteiro, Oliver J Furzer, Marc T Nishimura, Volkan Cevik, Kamil Witek, Jonathan D G Jones, Jeffery L Dangl, Detlef Weigel, Felix Bemm
Cell
5
(178 )
1260 -
1272.e14
(2019)
Li Wan, Kow Essuman, Ryan G Anderson, Yo Sasaki, Freddy Monteiro, Eui-Hwan Chung, Erin Osborne Nishimura, Aaron DiAntonio, Jeffrey Milbrandt, Jeffery L Dangl, Marc T Nishimura
Science
6455
(365 )
799 -
803
(2019)
Parras A; Anta H; Santos-Galindo M; Swarup V; Elorza A; Nieto-González J; Picó S; Hernández I; Díaz-Hernández J; Belloc E; Rodolosse A; Parikshak N; Peñagarikano O; Fernández-Chacón R; Irimia M; Navarro P; Geschwind D; Méndez R; Lucas J
Nature
560
(7719 )
441 -
446
(2018)
Barragán M; Pons J; Ferrer-Vaquer A; Cornet-Bartolomé D; Schweitzer A; Hubbard J; Auer H; Rodolosse A; Vassena R
Molecular Human Reproduction
23
(8 )
535 -
548
(2017)
Rinaldi, Lorenzo; Datta, Debayan; Serrat, Judit; Morey, Lluis; Solanas, Guiomar; Avgustinova, Alexandra; Blanco, Enrique; Ignacio Pons, Jose; Matallanas, David; Von Kriegsheim, Alex; Di Croce, Luciano; Aznar Benitah, Salvador
Cell Stem Cell
19
(4 )
491 -
501
(2016)

Services

The FGCF provides in-house genome-wide expression and mutation analysis services to researchers in public institutes and private companies. We are located in room S1C14 of the ‘Cluster I’ building at the ‘Parc Cientific de Barcelona’. If you are interested in a customised solution not listed below, please contact us at genomics@irbbarcelona.org. We look forward to learning about your projects and working side-by-side with you to overcome any experimental challenge.

If you are ready to submit your samples for analysis, please fill out the order in the ‘Policies and Forms’ tab below. Alternatively, feel free to reach out to us and schedule an appointment.

  • Consultancy and Experimental Design: Discuss your project with us and receive information about 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, thereby ensuring 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 regarding the collection of high-quality DNA and RNA samples. Our toolkit includes cost-efficient and highly effective methods for RNA extraction and cDNA amplification from 100 cells or even from only one oocyte.
  • Single-Cell Transcriptomics and Multiomics: In April 2021, our facility successfully deployed full 10X Genomics single-cell capabilities. In this regard, we offer:
    • Single-Cell Gene Expression Analysis.
    • Single-Cell ATAC-seq. Single-Cell Mutiome (simultaneous scRNA-seq + ATAC-seq).
    • Single-Cell Immune Profiling.
    • Targeted gene expression.
  • The 10X Genomics Chromium Controller can capture 100 to 10,000 cells per sample and process up to eight simultaneous samples. Before kickstarting your project, you can provide us with your single-cell suspensions. In only 10 minutes, you will obtain a cell QC informing on your cell processing and/or tissue dissociation workflow. Our team will further assist you with all the necessary steps to improve your sample preparation, obtain a service quote and schedule an appointment for sample submission.
  • Library Preparation for Illumina Next-Generation Sequencing (NGS): We employ fully validated and community-wide accepted procedures for library preparation, thereby ensuring consistent and reliable results. Nonetheless, whenever required, we will align our operating procedures with the specific needs of your project.
    • mRNA, lncRNA, miRNA, and sRNA Sequencing (RNA-seq): Bulk whole-transcriptome profiling using NGS technologies provides a comprehensive readout of transcript abundance, isoform diversity, as well as the discovery of novel transcripts and fusion genes. Our experienced staff will assist you with sample requisites, workflows, and sequencing strategies to meet the objectives of your project.
    • Whole-Genome Sequencing (WGS): Sequencing of the full genome of an individual allows for the identification of somatic or germline DNA variants.
    • ChIP-seq and RIP-seq: These approaches combines immunoprecipitation of chromatin (ChIP), or RNA (RIP), with NGS to identify protein-DNA, or protein-RNA, binding sites in a genome-wide manner. In recent years, the FGCF has supported dozens of ChIP-seq and RIP-seq projects. We will assist you through crosslinking, extraction, and fragmentation procedures to ensure that top quality libraries are obtained.
    • Hi-C: The FGCF has implemented a workflow for chromosome conformation capture and sequencing that allows researchers to map the spatial organisation of genomic DNA within the cell nuclei and identify conformational interactions between non-adjacent regions.
    • ATAC-seq: In this case, genome-wide chromatin accessibility is interrogated by transposase accessibility to uncover the extent and identity of regions prone to interact with transcription factors in cancer and other pathologies.
    • Targeted Sequencing: While WGS experiments might be your go-to option, their costs can still be prohibitive. Targeted approaches focus throughput, and therefore cost, on defined subsets of genomic regions, thus allowing greater sequencing depths for confident variant detection at lower prices
      • Amplicon Sequencing: PCR amplification of specific regions of interest reduces the target genomic space. Several methods are available for a comprehensive and careful panel design, thereby allowing you to multiplex hundreds or thousands of amplicons in a single reaction. Do not hesitate to reach out to obtain a custom design and quote.
      • Target Capture, or Sequence Capture and Enrichment: This alternative strategy reduces the sequenced genomic space by “capturing” regions of interest with custom biotinylated probes. Whole-Exome Sequencing is the most widespread Target Capture application. Our staff has extensive experience designing probes for target capture and would be pleased 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 mouse tumour organoid (MTO)-sorted cells or from only one oocyte.
  • Microarrays: Sample to results whole-genome gene expression analysis for a wide variety of experimental organisms using Genechip arrays.
  • DNA Methylation: Analysis of multiple loci 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. Runs must start within the working hours of the facility.
  • Clone collections: The FGCF has close to 200,000 clones for your reverse genetics needs, including:

More info

General

Initial consultation
Prior to starting your experiments, we invite you to discuss the experimental design with us.

Requirements for the services
Every service (clone delivery, microarray analysis, sequencing...) has its own specifications; details are available on the order forms of the specific services.

Who can perform projects with the FGC?
FGC is a facility open to everybody, researchers at IRB, in Barcelona, Spain, Europe and the rest of the world. We work with academia as well as with industry.

How is payment of services organised at the FGC?
In general, we have two prices, one for IRB researchers and one for everybody else.

Please find here the list of prices as well as the orders forms for all services:

 

1. List of prices

 

2. Order forms for IRB Barcelona users:

·       DNA-RNA extractions

·       Microarrays Affymetrix

·       Pico Profiling

·       Quality control

·       Reamplification

·       Sequencing

 

3. Order forms for external users:

·       DNA-RNA extractions

·       Microarrays Affymetrix

·       Pico Profiling

·       Quality control

·       Reamplification

·       Sequencing

 

For Spanish researchers: The government still does not give research institutions a tax-exempt status. Therefore, you have to add IVA to our prices.

Tools for Genomic Analysis

How long does it take until I get my results?
For smaller microarray projects (

For sequencing projects, a time frame of 3-6 weeks can be given for raw data delivery.

Which organisms can be analyzed?
In the field of Next Generation Sequencing, a reference genome of the organism must be available. Sequences are mapped to this reference genome.

Any organisms with a well annotated genome (or transcriptome) can be analyzed. In the field of microarrays, standard arrays can be purchased for many organisms. Affymetrix covers over 20 organisms, Agilent over 100. Arrays can also be customized for your favorite organism. This is usually easier with Agilent than with Affymetrix.

How do I best prepare my samples?
In general, a combination of organic phase extraction (phenol) with column purification (e.g. Qiagen) works best. These two completely different purification principles remove all kind of impurities. Protocols can be found and downloaded here. For miRNA analysis, do not use columns. Almost all of them remove short RNAs.

For very small samples (a few thousand cells), we propose a Picoprofiling service combining a specific protocol for RNA extraction with robust cDNA amplification method (See Pico-profiling order form).

I have doubts about the quality of my samples. Should I still submit them for analysis?
Before we start any expensive experiment like arrays or sequencing, we perform a broad range of quality controls. These include Nanodrop testing of purity, RNA integrity test on the Bioanalyzer, DNA or RNA specific quantification using the Qubit assays. If we have doubts about the samples, we will contact you for your decision "No or Go".

Alteration of Gene Expression

Who can request clones?
IRB has a single-use contract with Sigma and Open Biosystems, i.e. only IRB researchers and IBMB-CSIC researchers have access to the Sigma libraries; only IRB researchers have access to the Open Biosystems library. If you work outside of IRB, please contact Sigma and IRB administration to find out if these contracts can be modified to include your institution.

For which genes do you have shRNA or ORF clones?
Our shRNA clones cover approximately 75% of human and mouse refseq mRNAs, the ORF clones cover the same percentage of human genes. Access to shRNAs or ORF Clones libraries files to find and download the complete lists of available clones and corresponding genes.

I cannot open the clone lists because they are in xlsx-format.
The libraries contain more than 65,535 clones. Therefore, one needs Excel 2007 to show more than 65,535 rows.

I cannot find my favorite gene in your clone lists.
Our lists contain the official gene names as available on the NCBI website. At NCBI, go to the search field, click on gene and check if you used the official name.

How long does it take until I receive my clones?
Send us an email with your clone request, we tell you when tubes for bacterial inoculation should be delivered and you will receive the clones the same day of tube delivery. In toto, this takes 3 days max.

Group members

Senior Research Officer
Technical Officer

Do you want to be informed?

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