GeneCore Facility

About

Our mission is to promote and open advanced transcriptomics to all researchers by providing access to technologies with a low entry barrier. We are transcriptomics enthusiasts combining deep, interdisciplinary knowledge across biology, technology, and data science. We don't just hand over raw data; we partner with you from the initial experimental design to the final biological interpretation to ensure your project's success.

• 10+ Years of Experience: Decades of core facility expertise, pioneering single-cell and spatial transcriptomics, and advancing RNA-based biomarker research.
• Battle-Tested Workflows: Hundreds of successful experiments across diverse sample types and biological models. We have navigated the "painful learnings" so you don't have to.
• Global Network: Proudly partnering with world-class institutions and leading technology vendors.

Ready to unlock the full potential of your RNA samples? Contact us at genecore@ibt.cas.cz to discuss your ideas and learn how our expertise can accelerate your scientific discovery.

Acknowledgment:

We ask all users to acknowledge our services in any publications or presentations resulting from work conducted in the GeneCore Facility. Example acknowledgment: "We acknowledge the support of the GeneCore Facility at the Institute of Biotechnology of the Czech Academy of Sciences for [describe the service provided]."

We also welcome being informed of any new publications that have benefited from the support of the GeneCore Facility. These publications will be advertised on social media, highlighted during seminars given by GeneCore Facility members, and included in the list of supported works provided below.

Selected publications supported by the GeneCore Facility:

Bulk RNA-seq

• HIF-1α limits myocardial infarction by promoting mitophagy in mouse hearts adapted to chronic hypoxia. Alanova P, Alan L, Opletalova B, Bohuslavova R, Abaffy P, Matejkova K, Holzerova K, Benak D, Kaludercic N, Menabo R, Di Lisa F, Ostadal B, Kolar F, Pavlinkova G. Acta Physiol (Oxf). 2024 Sep;240(9):e14202. doi: 10.1111/apha.14202. Epub 2024 Jul 17. PMID: 39016532.
• Complement C3a treatment accelerates recovery after stroke via modulation of astrocyte reactivity and cortical connectivity. Stokowska A, Aswendt M, Zucha D, Lohmann S, Wieters F, Morán Suarez J, Atkins AL, Li Y, Miteva M, Lewin J, Wiedermann D, Diedenhofen M, Torinsson Naluai Å, Abaffy P, Valihrach L, Kubista M, Hoehn M, Pekny M, Pekna M. J Clin Invest. 2023 May 15;133(10):e162253. doi: 10.1172/JCI162253. PMID: 36995772.
• ISL1 controls pancreatic alpha cell fate and beta cell maturation. Bohuslavova R, Fabriciova V, Lebrón-Mora L, Malfatti J, Smolik O, Valihrach L, Benesova S, Zucha D, Berkova Z, Saudek F, Evans SM, Pavlinkova G. Cell Biosci. 2023 Mar 10;13(1):53.
• Glioblastoma and cerebral organoids: development and analysis of an in vitro model for glioblastoma migration. Fedorova V, Pospisilova V, Vanova T, Amruz Cerna K, Abaffy P, Sedmik J, Raska J, Vochyanova S, Matusova Z, Houserova J, Valihrach L, Hodny Z, Bohaciakova D. Mol Oncol. 2023 Apr;17(4):647-663. doi: 10.1002/1878-0261.13389. Epub 2023 Feb 18. PMID: 36744875.
• ISL1 is necessary for auditory neuron development and contributes toward tonotopic organization. Filova I, Pysanenko K, Tavakoli M, Vochyanova S, Dvorakova M, Bohuslavova R, Smolik O, Fabriciova V, Hrabalova P, Benesova S, Valihrach L, Cerny J, Yamoah EN, Syka J, Fritzsch B, Pavlinkova G. Proc Natl Acad Sci U S A. 2022 Sep 13;119(37):e2207433119. doi: 10.1073/pnas.2207433119. Epub 2022 Sep 8. PMID: 36074819.
• Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain. Androvic P, Kirdajova D, Tureckova J, Zucha D, Rohlova E, Abaffy P, Kriska J, Valny M, Anderova M, Kubista M, Valihrach L. Cell Rep. 2020 Jun 16;31(11):107777. doi: 10.1016/j.celrep.2020.107777. PMID: 32553170.

Single-cell RNA-seq

• NEUROD1 reinforces endocrine cell fate acquisition in pancreatic development. Bohuslavova R, Fabriciova V, Smolik O, Lebrón-Mora L, Abaffy P, Benesova S, Zucha D, Valihrach L, Berkova Z, Saudek F, Pavlinkova G. Nat Commun. 2023 Sep 9;14(1):5554. doi: 10.1038/s41467-023-41306-6. PMID: 37689751.
• Cortical glia in SOD1(G93A) mice are subtly affected by ALS-like pathology. Filipi T, Matusova Z, Abaffy P, Vanatko O, Tureckova J, Benesova S, Kubiskova M, Kirdajova D, Zahumensky J, Valihrach L, Anderova M. Sci Rep. 2023 Apr 21;13(1):6538. doi: 10.1038/s41598-023-33608-y. PMID: 37085528.
• Transient astrocyte-like NG2 glia subpopulation emerges solely following permanent brain ischemia. Kirdajova D, Valihrach L, Valny M, Kriska J, Krocianova D, Benesova S, Abaffy P, Zucha D, Klassen R, Kolenicova D, Honsa P, Kubista M, Anderova M. Glia. 2021 Nov;69(11):2658-2681. doi: 10.1002/glia.24064. Epub 2021 Jul 27. PMID: 34314531.

 Spatial transcriptomics

• Spatiotemporal transcriptomic map of ischemic brain injury. Zucha D, Abaffy P, Kirdajova D, Jirak D, Anderova M, Kubista M, Valihrach L. BioRxiv 2023.03.28.534553; doi: 10.1101/2023.03.28.534553.

Single-cell RT-qPCR

• The deletion of AQP4 and TRPV4 affects astrocyte swelling/volume recovery in response to ischemia-mimicking pathologies. Hermanova Z, Valihrach L, Kriska J, Maheta M, Tureckova J, Kubista M, Anderova M. Front Cell Neurosci. 2024 May 15;18:1393751. doi: 10.3389/fncel.2024.1393751. eCollection 2024. PMID: 38818517
• Compromised Astrocyte Swelling/Volume Regulation in the Hippocampus of the Triple Transgenic Mouse Model of Alzheimer's Disease. Tureckova J, Kamenicka M, Kolenicova D, Filipi T, Hermanova Z, Kriska J, Meszarosova L, Pukajova B, Valihrach L, Androvic P, Zucha D, Chmelova M, Vargova L, Anderova M. Front Aging Neurosci. 2022 Jan 27;13:783120. doi: 10.3389/fnagi.2021.783120. PMID: 35153718.
• High potassium exposure reveals the altered ability of astrocytes to regulate their volume in the aged hippocampus of GFAP/EGFP mice. Kolenicova D, Tureckova J, Pukajova B, Harantova L, Kriska J, Kirdajova D, Vorisek I, Kamenicka M, Valihrach L, Androvic P, Kubista M, Vargova L, Anderova M. Neurobiol Aging. 2020 Feb;86:162-181. doi: 10.1016/j.neurobiolaging.2019.10.009. Epub 2019 Oct 22. PMID: 31757575.
• Performance Comparison of Reverse Transcriptases for Single-Cell Studies. Zucha D, Androvic P, Kubista M, Valihrach L. Clin Chem. 2020 Jan 1;66(1):217-228. doi: 10.1373/clinchem.2019.307835. PMID: 31699702.
• A single-cell analysis reveals multiple roles of oligodendroglial lineage cells during post-ischemic regeneration. Valny M, Honsa P, Waloschkova E, Matuskova H, Kriska J, Kirdajova D, Androvic P, Valihrach L, Kubista M, Anderova M. Glia. 2018 May;66(5):1068-1081. doi: 10.1002/glia.23301. Epub 2018 Feb 2. PMID: 29393544.
• Generation of reactive astrocytes from NG2 cells is regulated by sonic hedgehog. Honsa P, Valny M, Kriska J, Matuskova H, Harantova L, Kirdajova D, Valihrach L, Androvic P, Kubista M, Anderova M. Glia. 2016 Sep;64(9):1518-31. doi: 10.1002/glia.23019. Epub 2016 Jun 24. PMID: 27340757.

Small RNA profiling

• Small RNA-Sequencing for Analysis of Circulating miRNAs: Benchmark Study. Androvic P, Benesova S, Rohlova E, Kubista M, Valihrach L. J Mol Diagn. 2022 Apr;24(4):386-394. doi: 10.1016/j.jmoldx.2021.12.006. Epub 2022 Jan 23. PMID: 35081459.
• Two-tailed RT-qPCR panel for quality control of circulating microRNA studies. Androvic P, Romanyuk N, Urdzikova-Machova L, Rohlova E, Kubista M, Valihrach L. Sci Rep. 2019 Mar 12;9(1):4255. doi: 10.1038/s41598-019-40513-w. PMID: 30862831.
• Two-tailed RT-qPCR: a novel method for highly accurate miRNA quantification. Androvic P, Valihrach L, Elling J, Sjoback R, Kubista M. Nucleic Acids Res. 2017 Sep 6;45(15):e144. doi: 10.1093/nar/gkx588. PMID: 28911110.

Services

We provide full-service support for every project: experimental design, sample processing, quality control (QC), library preparation, sequencing, and data analysis. By operating the broadest spectrum of advanced transcriptomics platforms in the CEE region, we ensure these comprehensive services are available and perfectly tailored to both academic and external commercial users.

Bulk Transcriptomics & Biomarkers

• Cost-Effective Profiling: 3’ profiling and DRUG-seq workflows optimized for high-throughput screening.
• Comprehensive RNA Analysis: Full-length, small RNA, and total RNA profiling.
• Biomarker Discovery: Specialized in RNA Fragmentomics and small RNA analysis.
• Actionable Data: Full data reports with advanced analysis included.

Single-Cell Transcriptomics

• Flexible Platforms: Supporting four major commercial platforms to meet diverse research needs.
• High Sensitivity: Smart-seq3xpress for in-depth analysis in 384-well plates.
• Versatile Inputs: Compatible with fresh, frozen, or fixed samples using single-cell and single-nucleus workflows.
• Interactive Results: Raw data analysis and export to intuitive, point-and-click analysis software included.

Spatial Transcriptomics

• Tissue Context: Map whole-transcriptome gene expression directly within tissue sections.
• Leading Technology: Access to all major sequencing-based platforms.
• Customizable: Resolution and array size tailored to your specific research needs, compatible with both fresh and fixed samples.

Sequencing & Additional Support

• Smart Sequencing: Priority access to major platforms, with sequencing depth adjusted to your real needs, not just platform availability.
• Cost Efficiency: Shared sequencing runs available to reduce overall costs.
• Core Lab Services: RNA extraction, QC (including Oxford Nanopore), RT-qPCR, and ddPCR.

Contact us at genecore@ibt.cas.cz to discuss your specific requirements and receive a customized quotation.

Please note: Final prices vary for internal, academic, and commercial users. Additionally, advanced transcriptomics is a rapidly developing field, with new and often more cost-effective solutions becoming available almost every quarter. Always consult with us first—we will help you navigate the latest options to find the most efficient and budget-friendly technology for your research.

Equipment

We equip your research with industry-leading platforms, delivering precision, speed, and unmatched scalability—from isolating single cells to executing massive sequencing runs.

• Sequencing at Any Scale: Priority access to next-generation powerhouses. We leverage the Illumina NovaSeq X for massive-scale experiments, alongside the Element AVITI 25 and MGI DNBSEQ-T1+ for highly versatile, cost-effective sequencing tailored to your project's exact needs.
• Single-Cell Precision: Advanced cell isolation and library construction. We utilize the CellenOne platform for ultra-precise, image-based single-cell sorting and nanoliter dispensing, paired with the 10x Genomics Chromium X and certified Illumina Accessories for robust, high-throughput droplet transcriptomics.
• High-Throughput Validation: Total flexibility for targeted gene expression. Our validation suite handles everything from massive microfluidic screening (Standard BioTools Biomark X9) and absolute quantification via Droplet Digital PCR (Bio-Rad QX200), to standard and 384-well qPCR (Bio-Rad CFX96 & CFX384).
• Uncompromising Quality Control: Exceptional data starts with perfect inputs. We strictly validate nucleic acid and library integrity using advanced capillary electrophoresis (Agilent Fragment Analyzer 5200) to guarantee your samples are sequencing-ready.

Supported Platforms & Kits

Bulk Transcriptomics / Bulková transkriptomika

• QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen)
• NEBNext® Ultra™ II RNA Library Prep Kit (New England Biolabs)
• NEBNext® Single Cell/Low Input RNA Library Prep Kit (New England Biolabs)
• RealSeq® Small RNA Library Prep Kit (RealSeq Biosciences)
• MERCURIUS™ BRB-seq Kits (Alithea Genomics)
• MERCURIUS™ DRUG-seq Kits (Alithea Genomics)
• RiboMarker® RNA Fragmentomics Kit (RealSeq Biosciences)

Single-Cell Transcriptomics / Single-cell transkriptomika

• Chromium Single Cell Gene Expression & Flex (10x Genomics)
• Illumina Single Cell 3' / PIPseq™ (Illumina / formerly Fluent Biosciences)
• Evercode™ Whole Transcriptome (QIAGEN / formerly Parse Biosciences)
• ScaleBio™ Single Cell RNA Kit (10x Genomics / formerly Scale Biosciences)
• Smart-seq3xpress (academic method/protocol)
• AVITI24™ Single-Cell Multiomics (Element Biosciences)

Spatial Transcriptomics / Prostorová Transkriptomika

• Visium Spatial Gene Expression (10x Genomics)
• Visium HD Spatial Gene Expression (10x Genomics)
• STOmics® / Stereo-seq (MGI/BGI)
• AVITI24™ Spatial Multiomics (Element Biosciences)

Sequencing / Sekvenování

• AVITI™ / AVITI24™ System (Element Biosciences)
• NovaSeq™ X Series (Illumina)
• DNBSEQ-T1+ (MGI/BGI)