The Genomics Core Facility at CABIMER provides a standardized portfolio of services for both external and internal researchers. This portfolio is flexible and can be adapted to the specific needs of researchers, provided that technical and economic feasibility allow.

Next-Generation Sequencing (NGS) Services – Illumina

With the Illumina sequencing platforms available at the lab (NextSeq500, NovaSeq6000 & iSeq200), users can process different number of samples and apply a broad range of sequencing methodologies across prokaryotic and eukaryotic organisms. The most commonly requested applications include:

• Transcriptomics (RNA SEQUENCING): Total RNA-Seq, mRNA-Seq, Small RNA-Seq, Ribo-Seq, RNA-Exome-Seq, targeted RNA-Seq…
• Single-Cell Sequencing (SINGLE-CELL): scRNA-Seq, scRNA-Seq PLEX, scATAC-Seq, scRNA-seq + ATAC-seq, CRISPR screening.
• Genome Sequencing (GENOME SEQUENCING): WGS, De novo sequencing, WES, custom panels, disease-specific panels.
• Epigenomics (EPIGENOMICS): ChIP-Seq, ATAC-Seq, MNase-Seq, 3C, 4C, RIP-Seq, DRIP-Seq, DRIPc-Seq.

For more details, please refer to the User Guide or contact the unit.

Single-Cell Analysis Service (scRNA-Seq, scATAC-Seq)

For single-cell applications, CABIMER’s Genomics Unit includes the Chromium Controller from 10X Genomics, which encapsulates individual cells in microspheres, allowing distinctive genetic labelling for high-throughput sequencing analysis.

Additionally, the Unit is equipped with Beckton Dickinson Rhapsody Xpress, a system based on depositing cells into micropore plates where specific beads enable individual genetic tagging.

To explore the full catalogue of applications, including those listed above, visit the websites of 10X Genomics and Beckton Dickinson. Sample requirements should be confirmed with the Genomics Unit, as information and methodologies are frequently updated.

Expression and Cytogenetic Microarray Services (Affymetrix)

Microarray technology enables structural and functional genomic analysis. Affymetrix microarrays provide highly reproducible and precise results.

Expression Microarrays (Refer to the User Guide)

• Traditional gene expression studies using 3’ IVT Arrays or Prime View microarrays.
• Whole-transcriptome analysis with Gene Arrays/Clariom S or Clariom D.
• Small-RNA microarrays for miRNA, snoRNA, scaRNA across more than 203 organisms.

Cytogenetic Microarrays (Refer to the User Guide)

• CytoScan Array: Detects chromosomal abnormalities, LOH, CNVs, mosaicism, etc.

Nucleic Acid Quality and Quantification Services

• Automated DNA/RNA quality analysis via Bioanalyzer/TapeStation.
• Fluorometric DNA/RNA quantification using Qubit™.

Scientific Applications Covered by These Services

• Single-Cell NGS: scRNA-Seq, scATAC-Seq, Multiome.
• High-throughput sequencing: RNA-Seq, ChIP-Seq, DNA-Seq, mutation screening, etc.
• Nucleic acid integrity analysis for RT-qPCR, sequencing, etc.
• Comparative gene expression profiling in eukaryotic and prokaryotic organisms.
• Splicing event detection and miRNA analysis.
• DNA-protein/DNA-RNA interaction studies.
• CNVs and chromosomal alterations in various biological samples.

Steps to Request a Service

1. Contact the Genomics Core Facility and follow the User Guide.
2. Complete the service form and submit it with samples.
3. Receive confirmation via email upon sample reception.
4. Preliminary quality control will be conducted and reported.
5. Refer to User Guides for submission and requirements.

For inquiries: eloisa.andujar@cabimer.es or monica.perez@cabimer.es Tel: +34 954 467828

To support scientific research and facilitate the development of advanced genomic studies, the Genomics Unit at CABIMER has recently expanded its technological infrastructure, incorporating state-of-the-art equipment, including:

• Next-Generation Sequencers:
  • NovaSeq 6000 (Illumina)
  • NextSeq 500 (Illumina)
  • iSeq 100 (Illumina)
• Single-Cell Analysis System:
  • RHAPSODY XPRESS SYSTEM (Beckton Dickinson)
  • CHROMIUM CONTROLLER (10X Genomics)
• Microarray Analysis Platforms:
  • GeneChip® Instrument System (Affymetrix), including:
    • Hybridization Oven Model 645
    • Fluidics Station 450
    • Scanner 3000 7G with autoloader for up to 40 cartridges and 532nm laser excitation
• Nucleic Acid Quality and Quantification Systems:
  • Bioanalyzer® 2100 (Agilent Technologies) with Vortexer MS S8/S9
  • TapeStation 4200 (Agilent Technologies)
  • Qubit 2.0 Fluorometric Quantification System (Life Technologies)
  • Nanodrop® ND-1000
• Robotic Systems for Automation and High-Throughput Processing:
  • RoToR HDA Colony Picker Robot (Singer Instruments)
  • Microlab Star Liquid Handling Robot (Hamilton)

Below is a list of publications in which the CABIMER Genomics Unit has participated:

1. Gay-Mimbrera J, Gómez-Arias PJ, Álvarez-Heredia P, Batista-Duharte A, Rivera-Ruiz I, Aguilar-Luque M, Juan-Cencerrado M, Mochón-Jiménez C, Cebrián-García A, Andújar-Pulido E, Pérez-Alegre M, Pera A, Ruano J. Integrated single-cellchromatin and transcriptomic analyses of peripheral immune cells in patients with alopecia areata. Frontiers in Immunology 2025, Jul doi: 10.3389/fimmu.2025.1565241
2. Gay-Mimbrera J , Lozano-Ojalvo D, Gómez-Arias PJ, Rivera-Ruiz I, Aguilar-Luque M, Mochón-Jiménez C, Andújar E, Pérez-Alegre M, Guttman-Yassky M, Ruano J. Comprehensive Single-Cell Chromatin and Transcriptomic Profiling of Peripheral Immune Cells in Non-Segmental Vitiligo (2025) Br J Dermatol . Jan 31:ljaf041. doi: 10.1093/bjd/ljaf041. Online ahead of print.
3. Casimiro-Soriguer CS, Pérez-Florido J, Robles EA, Lara M, Aguado A, Rodríguez Iglesias MA, Lepe JA, García F, Pérez-Alegre M, Andújar E, Jiménez VE, Camino LP, Loruso N, Ameyugo U, Vazquez IM, Lozano CM, Chaves JA, Dopazo J. The integrated genomic surveillance system of Andalusia (SIEGA) provides a One Health regional resource connected with the clinic.. Sci Rep. (2024) Aug 19;14(1):19200. 10.1038/s41598-024-70107-0.
4. Barrientos-Moreno M, Maya-Miles D, Murillo-Pineda M, Fontalva S, Pérez-Alegre M, Andújar E, Prado F.
   Transcription and FACT facilitate the restoration of replication-couple chromatin assembly defects.
   Sci Rep. 2023 Jul 14;13:11397.
   doi: 10.1038/s41598-023-38280-w.
5. Marchena Cruz E, Camino LP, Bhandari J, Silva S, Marqueta-Gracia JJ, Amdeen SA., Guillén-Mendoza C, García-Rubio M, Calderón-Montaño JM, Xue X, Luna R, Aguilera A.
   DDX47, MeCP2, and other functionally heterogeneous factors protect cells from harmful R loops.
   Cell Reports. 2023 Mar 28;42(3):112148.
   doi: 10.1016/j.celrep.2023.112148.
6. Gómez-Marín E, Posavec-Marjanović M, Zarzuela L, Basurto-Cayuela L, Guerrero-Martínez JA, Arribas G, Yerbes R, Ceballos-Chávez M, Rodríguez-Paredes M, Tomé M, Durán R, Buschbeck M, Reyes JC.
   The high mobility group protein HMG20A cooperates with the histone reader PHF14 to modulate TGFβ and Hippo pathways.
   Nucleic Acids Res. 2022 Sep 23;50(17):9838–9857.
   doi: 10.1093/nar/gkac766.
7. Loucera C, Pérez-Florido J, Casimiro-Soriguer CS, Ortuño FM, Carmona R, Bostelmann G, Martínez-González LJ, Muñoyerro-Muñiz D, Villegas-Portero R, Rodríguez-Baño J, Romero-Gómez M, Lorusso N, García-León FJ, Navarro-Marí JM, Camacho-Martínez P, Merino Díaz L, Salazar A, Viñuela L, The Andalusian COVID-19 Sequencing Initiative, Lepe JA, García F, Dopazo J.
   Assessing the Impact of SARS-CoV-2 Lineages and Mutations on Patient Survival.
   Viruses. 2022 Aug 27;14(9):1893.
   doi: 10.3390/v14091893.
8. Serrano-Pérez E, Romero-Losada AB, Morales-Pineda M, García-Gómez ME, Couso I, García-González M, Romero-Campero FJ.
   Transcriptomic and Metabolomic Response to High Light in the Charophyte Alga Klebsormidium nitens.
   Front Plant Sci. 2022 May 6;13:855243.
   doi: 10.3389/fpls.2022.855243.
9. Sánchez-Escabias E, Guerrero-Martínez JA, Reyes JC.
   Co-transcriptional splicing efficiency is a gene-specific feature that can be regulated by TGFβ.
   Commun Biol. 2022 5:277. Published online Mar 28.
   doi:10.1038/s42003-022-03224-z.
10. Arroyo N, Villamayor N, Díaz I, Carmona R, Ramos-Rodríguez M, Muñoz-Chápuli R, Pasquali L, Tosacno MG, Martín F, Cano DA, Rojas A.
    GATA4 induces liver fibrosis regression by deactivating hepatic stellate cells.
    JCI Insight. 2021 Dec 8;6(23):e150059.
    doi: 10.1172/jci.insight.150059.
11. Alenda C, Rojas E, Valor LM.
    FFPE samples from cavitational ultrasonic surgical aspirates are suitable for RNA profiling of gliomas.
    PLoS One. 2021 Jul 22;16(7):e0255168.
    doi: 10.1371/journal.pone.0255168.
12. Payán-Bravo L, Fontalva S, Peñate X, Cases I, Guerrero-Martínez JA, Pareja-Sánchez Y, Odrioza-Gil Y, Lara E, Jimeno-González S, Suñé C, Muñoz-Centeno MC, Reyes JC, Chávez S.
    Human prefoldin modulates co-transcriptional pre-mRNA splicing.
    Nucleic Acids Res. 2021 Jun 21;49(11):6267–6280.
    doi: 10.1093/nar/gkab446.
13. Bayona-Feliu A, Barroso S, Muñoz S, Aguilera A.
    The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts.
    Nature Genetics. 2021 May 13;53, 1050–1063.
    doi: 10.1038/s41588-021-00867-2.
14. Lorenzo PI, Martín-Vázquez E, López-Noriega L, Fuente-Martín E, Mellado-Gil JM, Franco JM, Cobo-Vuilleumier N, Guerrero-Martínez JA, Romero-Zerbo SY, Pérez-Cabello JA, Rivero S, Campos-Caro A, Lachaud CC, Crespo Barreda A, Aguilar-Diosdado M, García Fuentes E, Martín-Montalvo A, Álvarez-Dolado M, Martín F, Rojo-Martínez G, Pozo D, Bermúdez-Silva FJ, Comaills V, Reyes JC, Gauthier BR.
    The metabesity factor HMG20A potentiates astrocyte survival and reactive astrogliosis preserving neuronal integrity.
    Theranostics. 2021 May 12;11(14):6983–7004.
    doi: 10.7150/thno.57237.
15. Álvarez-Amor L, Luque Sierra A, Cárdenas A, López-Bermudo L, López-Beas J, Andújar E, Pérez-Alegre M, Gallego-Durán R, Varela LM, Martin-Montalvo A, Berná G, Rojas A, Robles-Frías MJ, Hmadcha A, Romero-Gómez M, Kleemann R & Martín F
    Extra virgin olive oil improved body weight and insulin sensitivity in high fat diet-induced obese LDLr-/-Leiden mice without attenuation of steatohepatitis.
    Scientific Reports. 2021 Apr 15;11 (1): 8250
    doi: 101038/s41598-021-87761-3..
16. Herrero-Ruiz A, Martínez-García PM, Terrón-Bautista J, Millán-Zambrano G, Lieberman JA, Jimeno-González S, Cortés-Ledesma F
    Topoisomerase IIα represses transcription by enforcing promoter-proximal pausing.
    Cell Rep. 2021 Apr 13;35(2):108977. doi:10.1016/j.celrep.2021.108977.
17. Sessa G, Gómez-González BM, Silva S, Pérez-Calero C, Beaurepere R, Barroso S, Martineau S, Martin C, Ehlén Å, Martínez JS, Lombard B, Loew D, Vagner S, Aguilera A, Carreira A.
    BRCA2 promotes DNA-RNA hybrid resolution by DDX5 helicase at DNA breaks to facilitate their repair by homologous recombination.
    EMBO J. 2021 Apr 1;40(7):e106018. doi:10.15252/embj.2020106018.
18. Marín-Aguilar F, Castejón-Vega B, Alcocer-Gómez E, Lendines-Cordero D, Cooper MA, de la Cruz P, Andújar-Pulido E, Pérez-Alegre M, Muntané J, Pérez-Pulido AJ, Ryffel B, Robertson AAB, Ruiz-Cabello J, Bullón P, Cordero MD
    NLRP3 inflammasome inhibition by MCC950 in aged mice improves health via enhanced autophagy and PPARα activity.
    J Gerontol A Biol Sci Med Sci. 2020 Jul 13;75(8):1457-1464. doi:10.1093/gerona/glz239.
19. Salto R, Girón MD, Manzano M, Martín MJ, Vílchez JD, Bueno-Vargas P, Cabrera E, Pérez-Alegre M, Andújar E, Rueda R, Lopez-Pedrosa JM
    Programming Skeletal Muscle Metabolic Flexibility in Offspring of Male Rats in Response to Maternal Consumption of Slow Digesting Carbohydrates during Pregnancy.
    Nutrients. 2020 Feb 19;12(2):528. doi:10.3390/nu12020528.
20. Salas-Armenteros I, Barroso SI, Rondón AG, Pérez M, Andújar E, Luna R, Aguilera A
    Depletion of the MFAP1/SPP381 Splicing Factor Causes R-Loop-Independent Genome Instability.
    Cell Rep. 2019 Aug 6;28(6):1551-1563.e7. doi:10.1016/j.celrep.2019.07.010.
21. Maya-Miles D, Andújar E, Pérez-Alegre M, Murillo-Pineda M, Barrientos-Moreno M, Cabello-Lobato M, Gómez-Marín E, Morillo-Huesca M, Prado F
    Crosstalk between chromatin structure, cohesin activity and transcription.
    Epigenetics & Chromatin. 2019 Jul 22;12(1):47. doi:10.1186/s13072-019-0293-6.
22. Barroso R, García-Mauriño SM, Tomás-Gallardo L, Andújar E, Pérez-Alegre M, Santero E, Canosa I
    The CBRB regulon: Promoter dissection reveals novel insights into the CbrAB expression network in Pseudomonas putida.
    PLoS ONE. 2018 Dec;13(12):e0209191. doi:10.1371/journal.pone.0209191.
23. González-Arranz S, Cavero S, Morillo-Huesca M, Andújar E, Pérez-Alegre M, Prado F, San-Segundo P
    Functional impact of the H2AZ histone variant during meiosis in Saccharomyces cerevisiae.
    Genetics. 2018 Aug;209(4):997-1015. doi:10.1534/genetics.118.301110.

You can download the following guides and forms by clicking on the links:
GUIDES

• NGS Illumina User Guide  (PDF)
• User Guide for Quality and/or Quantity Analysis of Nucleic Acids (PDF)
• Expression Microarray User Guide (Affymetrix) (PDF)
• Cytogenetics Microarray User Guide (Affymetrix) (PDF)

FORMS

• NGS-Illumina Request Form  (.doc)
• Microarray Request Form  (.doc)
• Quality/Quantity Analysis of Nucleic Acids Request Form  (.doc)
• Data Analysis Request Form  (.doc)

You can check the rates at this link or contact us at this link or contact us at

phone number +34 95 446 7828 or via email at  eloisa.andujar@cabimer.es, monica.perez@cabimer.es.