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Description
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The main objective of the Cabimer Genomics Unit is to provide services to both internal and external researchers through various technological approaches related to Functional Genomics.
The Genomics Core Facility at CABIMER is dedicated to providing comprehensive support to researchers (both internal and external), through different technological approaches related to Functional Genomics.
In recent years, DNA microarrays paved the way for Next-Generation Sequencing (NGS) technologies—and more recently and revolutionarily, Single-Cell approaches—have emerged as critical tools for genome and transcriptome analysis. To facilitate such cutting-edge research, CABIMER has implemented and integrated multiple platforms (Affymetrix, Illumina, 10X Genomics and BD Rhapsody), which are continuously evolving demands of the scientific community, supporting research in gene expression, chromatin dynamics, epigenetics, and beyond.
Services
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.
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.
Expression and Cytogenetic Microarray Services (Affymetrix). Microarray technology enables structural and functional genomic analysis. Affymetrix microarrays provide highly reproducible and precise results.
- Expression microarrays: 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: 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.
Equipment
- 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 and 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).
Data analysis of the sequencing output is offered by the Bioinformatics Unit at CABIMER.
Staff
- Cristina González Aguilera – Scientific Lead
- Eloísa Andújar Pulido – Technical Lead
- Victoria Jiménez Santos – Technical Lead
- Mónica Pérez Alegre – Technical Lead
- Lola Pérez de Camino Cantos – Technical Lead
How to request a service
- Contact the Genomics Core Facility and follow the User Guide.
- Complete the service form and submit it with samples.
- Receive confirmation via email upon sample reception.
- Preliminary quality control will be conducted and reported.
Contact: eloisa.andujar@cabimer.es, monica.perez@cabimer.es – Tel: +34 954 467828.
Fees 2026
Approved by CABIMER's Governing Board on 18 June 2026 (full price list, PDF). Price per run unless stated otherwise.
NGS – NextSeq 500
- Mid Output, 150 cycles, 130M reads: 1,142 € (CABIMER) / 1,256 € (institutions) / 1,370 € (external)
- Mid Output, 300 cycles, 130M reads: 1,834 € (CABIMER) / 2,017 € (institutions) / 2,200 € (external)
- High Output, 75 cycles, 400M reads: 1,662 € (CABIMER) / 1,828 € (institutions) / 1,994 € (external)
- High Output, 150 cycles, 400M reads: 3,204 € (CABIMER) / 3,524 € (institutions) / 3,844 € (external)
- High Output, 300 cycles, 400M reads: 5,022 € (CABIMER) / 5,525 € (institutions) / 6,027 € (external)
NGS – NovaSeq 6000
- SP, 100 cycles, 800M reads: 2,055 € (CABIMER) / 2,260 € (institutions) / 2,466 € (external)
- SP, 300 cycles, 800M reads: 3,551 € (CABIMER) / 3,907 € (institutions) / 4,262 € (external)
- SP, 500 cycles, 800M reads: 5,012 € (CABIMER) / 5,514 € (institutions) / 6,015 € (external)
- S1, 100 cycles, 1,600M reads: 3,781 € (CABIMER) / 4,159 € (institutions) / 4,537 € (external)
- S1, 200 cycles, 1,600M reads: 4,804 € (CABIMER) / 5,284 € (institutions) / 5,764 € (external)
- S1, 300 cycles, 1,600M reads: 5,876 € (CABIMER) / 6,464 € (institutions) / 7,051 € (external)
- S2, 100 cycles, 4,100M reads: 6,537 € (CABIMER) / 7,191 € (institutions) / 7,845 € (external)
- S2, 200 cycles, 4,100M reads: 8,197 € (CABIMER) / 9,017 € (institutions) / 9,837 € (external)
- S2, 300 cycles, 4,100M reads: 10,554 € (CABIMER) / 11,609 € (institutions) / 12,664 € (external)
- S4, 35 cycles, 10 billion reads: 10,303 € (CABIMER) / 11,333 € (institutions) / 12,364 € (external)
- S4, 200 cycles, 10 billion reads: 13,618 € (CABIMER) / 14,980 € (institutions) / 16,342 € (external)
- S4, 300 cycles, 10 billion reads: 15,235 € (CABIMER) / 16,758 € (institutions) / 18,282 € (external)
- SP 1-lane, 200 cycles, 400M reads: 1,496 € (CABIMER) / 1,646 € (institutions) / 1,796 € (external)
- S1 1-lane, 100 cycles, 800M reads: 2,027 € (CABIMER) / 2,230 € (institutions) / 2,433 € (external)
- S2 1-lane, 100 cycles, 2,000M reads: 3,406 € (CABIMER) / 3,746 € (institutions) / 4,087 € (external)
- S2 1-lane, 200 cycles, 2,000M reads: 4,236 € (CABIMER) / 4,659 € (institutions) / 5,083 € (external)
- Extra sequencing SP/S1/S2 2D-lane: 281 € (CABIMER) / 309 € (institutions) / 337 € (external)
- Extra sequencing S4 4D-lane: 564 € (CABIMER) / 620 € (institutions) / 677 € (external)
- Quality control (pre-sequencing): 26.3 € (CABIMER) / 28.9 € (institutions) / 31.6 € (external)
NGS – iSeq 100
- i1, 300 cycles, 4M reads: 684 € (CABIMER) / 798 € (institutions) / 912 € (external)
Libraries (per sample)
- mRNA-Seq: 77.24 € (CABIMER) / 84.48 € (institutions) / 101.38 € (external)
- Total RNA-Seq: 111.77 € (CABIMER) / 139.71 € (institutions) / 167.65 € (external)
- Total RNA-Seq Microbiome: 114.42 € (CABIMER) / 143.02 € (institutions) / 171.62 € (external)
- Total RNA-Seq Low Input: 235.96 € (CABIMER) / 294.95 € (institutions) / 353.93 € (external)
- smallRNA-Seq: 135.41 € (CABIMER) / 148.10 € (institutions) / 177.72 € (external)
- WGS (Whole Genome Sequencing): 63.53 € (CABIMER) / 76.10 € (institutions) / 91.32 € (external)
- ChIP-Seq/MNase-Seq: 100.68 € (CABIMER) / 125.85 € (institutions) / 151.02 € (external)
- DNA-Seq (PCR-free): 60.67 € (CABIMER) / 72.68 € (institutions) / 87.22 € (external)
- Ribo-Seq: 135.41 € (CABIMER) / 148.10 € (institutions) / 177.72 € (external)
- Exome (human): 76.10 € (CABIMER) / 95.13 € (institutions) / 114.16 € (external)
- Metagenomics (shotgun): 63.53 € (CABIMER) / 76.10 € (institutions) / 91.32 € (external)
- Single cell RNA 10x (scRNA-Seq): 3,073.69 € (CABIMER) / 3,381.06 € (institutions) / 3,688.43 € (external)
- Single cell ATAC 10x (scATAC-Seq): 2,968.16 € (CABIMER) / 3,264.97 € (institutions) / 3,561.79 € (external)
- Multiome 10x (scRNA + scATAC): 4,949.27 € (CABIMER) / 5,444.20 € (institutions) / 5,939.12 € (external)
- Specialist hour: n/a (CABIMER) / 40.00 € (institutions) / 50.00 € (external)
- Other libraries (incl. single cell BD Rhapsody): ask the unit.
Microarrays and quality control
- Microarrays (plus consumables): 50.00 € (CABIMER) / 70.00 € (institutions) / 90.00 € (external)
- Bioanalyzer RNA nano (1-6 / >6 samples): 6.00 € / 4.00 € (CABIMER) / 9.00 € / 7.00 € (institutions) / 11.00 € / 9.00 € (external)
- Bioanalyzer RNA pico (1-6 / >6 samples): 7.00 € / 5.00 € (CABIMER) / 10.00 € / 8.00 € (institutions) / 12.00 € / 10.00 € (external)
- Bioanalyzer DNA HS (1-6 / >6 samples): 11.00 € / 7.00 € (CABIMER) / 14.00 € / 10.00 € (institutions) / 16.00 € / 12.00 € (external)
- Qubit quantification: 1.50 € (CABIMER) / 3.00 € (institutions) / 5.50 € (external)
- Microarray basic analysis (per condition, 3-9 samples): 90.00 € (CABIMER) / 360.00 € (institutions) / 720.00 € (external)
- Microarray functional analysis: depending on the project.
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