GeneCore Facility

About us

GeneCore Facility is a leading research laboratory providing cutting-edge transcriptomic services. With over 18 years of experience in the field, we specialize in bulk, single-cell and spatial transcriptomics, providing comprehensive support from experimental design to data analysis.

Our Expertise

At the GeneCore Facility, we offer a wide range of techniques for transcriptomic analysis, from examining activity of several genes in a few samples to analyzing whole transcriptome in millions of cells. After an initial consultation, we propose the best experimental solutions tailored to your research questions and budget. Through rigorous sample quality control and validated protocols, we ensure accurate and reliable results, delivering high-quality data for your research needs.

Our Mission

The primary goal of the GeneCore Facility is to provide cutting-edge transcriptomic technologies to the Czech scientific community and support groundbreaking research. We work closely with leading scientists and technology providers to offer exceptional services using the latest advancements in the field.

Supporting Research Excellence

Aligned with the mission and vision of the Institute of Biotechnology at the Czech Academy of Sciences, our services contribute to diverse research initiatives, paving the way for next-generation medicines and innovative biotechnologies.

Contact us

Partner with the GeneCore Facility to unlock the full potential of transcriptomic analysis and accelerate your research. Contact us at genecore@ibt.cas.cz to discuss your project requirements and learn how our expertise can drive scientific discovery and innovation.

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.

Our services encompass the entire experimental workflow, including experimental design, sample preparation and quality control, library preparation, sequencing, and data analysis. These services are available to both academic and external commercial users.

Consultation and Experimental Design
Every successful project begins with a robust experimental design.

• Assistance with method selection.
• Guidance on sample collection.
• Recommendation on quality control tools.
• Option for pilot experiments.
• Data analysis options.

Sample Preparation, Processing, and Quality Control
Comprehensive protocol to ensure high-quality data for your research.

• RNA extraction.
• Assessment of RNA quality and quantity (using Nanodrop, Qubit, Fragment Analyzer).
• RT-qPCR-based quality control.
• Cell viability assessment.

Reverse Transcription Quantitative PCR (RT-qPCR)
Standardized targeted mRNA analysis for various research needs.

• Primer design and validation.
• Quality control assays.
• Bulk and single-cell RNA profiling (Bio-Rad CFX96 and CFX384).
• High-throughput mRNA profiling (BioMark).

Digital Droplet PCR
Absolute quantification of target DNA or RNA molecules.

• Assay design and validation.
• QX200 Droplet Digital PCR System from Bio-Rad.

Bulk Transcriptomics
Whole transcriptome analysis in tissue or cell culture samples.

• QuantSeq 3’ mRNA-Seq V2 Library Prep Kit from Lexogen (link) for 3’ end expression profiling.
• NEBNext® Ultra™ II Directional RNA Library Prep Kit (link) for whole transcriptome analyses.
• From 1 400 CZK per sample.*

Small RNA Profiling
Targeted and whole small transcriptome analysis.

• Two-tailed RT-PCR (link) for individual miRNA analysis.
• RealSeq Small RNA Library Kit from RealSeq Biosciences (link) for whole small transcriptome analysis.
• From 3 000 CZK per sample.*

Single-Cell Transcriptomics
Whole transcriptome analysis at the individual cell level, scalable to any project size.

• Evercode from Parse Biosciences (link) for large-scale projects.
• Chromium Single Cell Gene Expression from 10x Genomics (link) for medium-sized experiments.
• PIPseq V from FluentBiosciences (link) for various project sizes.
• Smart-seq3xpress plate-based technology (link) for rare cells analysis.
• From 10 000 CZK per sample.*

Spatial Transcriptomics
Whole transcriptome analysis with spatial resolution.

• Visium Spatial Gene Expression from 10x Genomics (link) for whole transcriptome spatial analysis.
• From 60 000 CZK per sample.*

Sequencing Services

• Cost-effective sequencing using the latest NovaSeqX platform (link)**.
• Option for shared sequencing run.
• From 22 000 CZK per 1B reads.*
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Data Analysis

• Support with data preparation and basic analysis.
• In-house data analysis for bulk transcriptomics.
• Point-and-click software for complex single-cell data analysis.

* Informative prices are provided excluding VAT, with detailed quotations available upon request at genecore@ibt.cas.cz. Final prices depend on the number of samples and vary for internal users, academic users, and external commercial users.

** Sequencing services are provided using the NovaSeqX platform, located in the BIOCEV building and maintained by the First Faculty of Medicine, Charles University.

CFX96 // BioRad // qPCR

CFX384 // BioRad // qPCR

QX200 // Biorad // dPCR

Biomark // Fluidigm // high-throughput qPCR

EpMotion P5073 // Eppendorf // pipetting robot

Fragment Analyzer 5200// Agilent // capillary electrophoresis for QC of nucleic acids

CellenOne // Cellenion // single cell sorter and nanodispenser

Chromium Controller // 10x Genomics // Library preparation for single-cells

PIPseq T2 3’ Single Cell Equipment // FluentBiosciences // Certified library preparation accesories