Centro Andaluz de Biología Molecular y Medicina Regenerativa
Genomics Unit

The Genomics Core Facility at Cabimer provides a wide-ranging of genomics services for local and international researchers including Next Generation Sequencing (massive or deep sequencing) and advisement for experimental design and bioinformatics data analysis.

Genomics is an area of ​​Biology focused on whole genome studies. Genomes (genes and non-coding regions, proteins binding to DNA, nucleosomes…) are the characters in charge of cell plasticity, evolution and differentiation. Functional Genomics try to understand the role of the whole genome on a global approach and its impact on the development and physiology of an organism.

The Genomics Core Facility at Cabimer provides a wide diversity of methods for DNA and RNA analyses with high-throughput technologies and systems. Available equipment include liquid handling robots to automate pipeting task, DNA quantification and quality control with Qubit and Bioanalyzer, real-time PCR, a high-content imaging system (ImageXpress Micro), Affymetrix and Agilent microarray platforms and two next-generation sequencing system: NextSeq500 from Illumina and PGM from Ion-Torrent. The result is a complete and highly flexible open service performing a broad range of applications from targeted RNA/DNA and whole-exome or genome sequencing.

The services described are intended to cover, among others, the following scientific applications:

  • NGS SEQUENCING: RNA-Seq, ChIP-Seq, DNA-Seq, ATAC-Seq, CNV, circulating DNA, cancer studies, hereditary and custom diseases….
  • QUALITY ANALYSIS (integrity) and QUANTIFICATION OF DNA and RNA as a preliminary study for RT-qPCR, sequencing, microarrays, etc.
  • COMPARATIVE STUDY OF GENE EXPRESSION PROFILES (eukaryotics and prokaryotics)
  • STUDIES OF SPLICING EVENTS ASSOCIATED WITH GENE EXPRESSION
  • ANALYSIS OF miRNA (pre-miRNA, snoRNA, lncRNA …) related to gene expression
  • STUDIES OF INTERACTION DNA-PROTEIN (ChIP-on-chip, ChIP-Seq …).
  • DETECTION OF VARIATIONS IN COPY NUMBER AND CHROMOSOMAL ALTERATIONS (CNVs and SNPs) in cell cultures, prenatal samples, fresh and FFPE samples of humans (including tumors), study of included LOH (molecular cytogenetics), CGH, studies of trios, etc.
  • LARGE SCALE AUTOMATED SCREENING THROUGH FLUORESCENCE MICROSCOPY (high content imaging).
  • AUTOMATION OF PROTOCOLS for handling liquid solutions with a large number of samples: preparation of PCR plates (96-384) or ELISA, dilutions, screening protocols, collections copy, DNA / RNA extraction.

To apply for some of these services, you must follow the following steps:

  1. Ask for the Genomics Unit (experimental design) and follow the instructions on the User Guides.
  2. Fill in the Request for the appropriate service form and send it with the samples
  3. Upon receipt of the samples/data, a confirmation email will be sent to the user, indicating the possible start date for analysis (depend on availability of the service).
  4. Previous to the analysis, a preliminary control of the samples / data will be made and the user will be notified of the result via email.
  1. A genome-wide screening uncovers the role of CCAR2 as an antagonist of DNA end resection (2016). López-Saavedra A, Gómez-Cabello D, Domínguez-Sánchez MS, Mejías-Navarro F, Fernández-Ávila MJ, Dinant C, Martínez-Macías MI, Bartek J, Huertas P. Nat Commun. 2016 Aug 9;7:12364.
  2. Excess of Yra1 RNA-Binding Factor Causes Transcription-Dependent Genome Instability, Replication Impairment and Telomere Shortening (2016). Gavaldá S, Santos-Pereira JM, García-Rubio ML, Luna R, Aguilera A. PLoS Genet. 2016 Apr 1;12(4).
  3. The chromatin Remodeler CHD8 is required for activation of progesterone receptor-dependent enhancers (2015). Ceballos-Chávez M, Subtil-Rodríguez A, Giannopoulou EG, Soronellas D, Vázquez-Chávez E, Vicent GP, Elemento O, Beato M,Reyes JC. PLoS Genet. 2015 Apr 20;11(4):e1005174.
  4. Survival of human circulating antigen-induced plasma cells is supported by plasma cell-niche cytokines and T follicular helper lymphocytes(2015). Ramos-Amaya A, Rodríguez-Bayona B, López-Blanco R, Andújar E, Pérez-Alegre M, Campos-Caro A, Brieva JA. J Immunol. Feb 1;194(3):1031-8.
  5. Defective histone supply causes changes in RNA polymerase II elongation rate and cotranscriptional pre-mRNA splicing (2015). Jimeno-González S, Payán-Bravo L, Muñoz-Cabello AM, Guijo M, Gutierrez G, Prado F, Reyes JC. Proc Natl Acad Sci U S A. Dec 1;112(48):14840-5.
  6. R Loops Are Linked to Histone H3 S10 Phosphorylation and Chromatin Condensation (2013). Castellano-Pozo M, Santos-Pereira JM, Rondón AG, Barroso S, Andújar E, Pérez-Alegre M, García-Muse T, Aguilera A. Mol Cell. Nov 21;52(4):583-90.
  7. Zebularine regulates early stages of mESC differentiation: effect on cardiac commitment (2013). Horrillo A, Pezzolla D, Fraga MF, Aguilera Y, Salguero-Aranda C, Tejedo JR, Martin F, Bedoya FJ, Soria B, Hmadcha A. Cell Death Dis. Apr 4;4:e570.
  8. Gene expression profiles in the cerebellum of transgenic mice over expressing the human FMR1 gene with CGG repeats in the normal range (2012). Fernández JJ, Martínez R, Andújar E, Pérez-Alegre M, Costa A, Bonilla-Henao V, Sobrino F, Pintado CÓ, Pintado E. Genet Mol Res. Mar 1;11(1):467-83.
  9. Nab2 functions in the metabolism of RNA driven by polymerases II and III (2011). Gonzalez-Aguilera C, Tous C, Babiano R, De la Cruz J, Luna R, Aguilera A. Mol Biol Cell. Aug 1;2(15):2729-40.
  10. Zim17/Tim15 links mitochondrial iron-sulfur cluster biosynthesis to nuclear genome stability (2011). Díaz de la Loza MD, Gallardo M, García-Rubio ML, Izquierdo A, Herrero E, Aguilera A, Wellinger RE. Nucleic Acids Res. Aug;39(14):6002-15. Epub 2011 Apr 21.
  11. Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles (2011). Belen Gómez-Gonzalez, Marıa Garcıa-Rubio, Rodrigo Bermejo, Helene Gaillard, Katsuhiko Shirahige, Antonio Marın, Marco Foiani and Andres Aguilera. The EMBO Journa.l Jun 24;30(15):3106-19. doi: 10.1038/emboj.2011.206.
  12. Gene expression pattern in swine neutrophils after lipopolysaccharide exposure: a time course comparison (2011). Gema Sanz-Santos, Ángeles Jiménez-Marín, Rocío Bautista, Noé Fernández, Gonzalo M Claros, Juan J Garrido. BMC Proceedings Jun 3; 5(Suppl 4):S11.
  13. Differential expression of THOC1 and ALY mRNP biogenesis/export factors in human cancers (2011). Maria S Dominguez-Sanchez, Carmen Saez, Miguel A Japon, Andres Aguilera and Rosa Luna. BMC Cancer, 11:77doi:10.1186/1471-2407-11-77.
  14. The SWR1 Histone Replacement Complex Causes Genetic Instability and Genome-Wide transcription Misregulation in the Absence of H2A.Z (2010). Morillo-Huesca M, Clemente-Ruiz M, Andujar E, Prado F. T. PLoS ONE 5(8): e12143. doi:10.1371/journal.pone.0012143.
  15. Global Gene Expression Profiling of Pheripheral Blood Pancreas Adenocarcinoma Patients to Determine Potential BiomarkerS to Treatment Response (2010). O. Caba, P. Álvarez, J. Prados, R. Ortiz, C. Melguizo, F. Rodríguez-Serrano, J. R. Delgado, I. Rojas, J. Pérez-Florido, A. Prieto, A. Aránega, MedMol Research Reports (MMR), doi: 10.4428/MMRR.a.201005003.
  16. Histone h2a.z and homologs of components of the SWR1 complex control immunity in Arabidopsis (2008). R. March-Díaz, M. García-Domínguez, J. Lozano-Juste, J. León, F.J. Florencio and J.C. Reyes. Plant Journal. 53:475-487.