Gene Core

We are an academic facility providing services specializing in single-cell profiling and spatial transcriptomics.






GeneCore offers service in the field of single-cell and spatial transcriptomics.

We have 18 years experience with single-cell profiling.

At our state-of-the-art service laboratory, we specialize in cutting-edge techniques for RNA library preparation, empowering researchers to uncover the intricate genetic mechanisms behind biological processes.

With our expertise in the RNA analysis, we offer comprehensive analysis of individual cells, enabling a deeper understanding of cellular diversity, heterogeneity and gene expression patterns.

Our service laboratory is equipped with advanced spatial transcriptomic technology, allowing researchers to visualize gene expression within intact tissue samples, unraveling the spatial organization of cellular activity.

We take pride in delivering accurate and reliable results through our meticulous RNA sequencing workflows, ensuring high-quality data for your research needs.

Collaborating with leading scientists and utilizing the latest sequencing platforms, our service laboratory is committed to providing exceptional services in the field of RNA sequencing, single cell RNA sequencing, and spatial transcriptomics.










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 RNA-seq

  • 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.
  • 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.

Bulk RNA-seq

  • 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.


  • 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.
  • Tutorial: Guidelines for Single-Cell RT-qPCR. Zucha D, Kubista M, Valihrach L. Cells. 2021 Sep 30;10(10):2607. doi: 10.3390/cells10102607. PMID: 34685587.
  • 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

miRNA 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.
  • Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis. Benesova S, Kubista M, Valihrach L. Diagnostics (Basel). 2021 May 27;11(6):964. doi: 10.3390/diagnostics11060964. PMID: 34071824.
  • Circulating miRNA analysis for cancer diagnostics and therapy. Valihrach L, Androvic P, Kubista M. Mol Aspects Med. 2020 Apr;72:100825. doi: 10.1016/j.mam.2019.10.002. Epub 2019 Oct 18. PMID: 31635843.
  • 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.
Kulinich Viktoriia, Bc.
Langerová Lucie, Ing.
Kubista Mikael, prof. Dr., Ph.D.
Mášová Alice, RNDr., Ph.D.
Rohlová Eva, Ing.


  • Sample extraction and nucleic acid quality control
  • Assay design (qPCR and dPCR)
  • qPCR and high-throughput qPCR (gene expression, genotyping)
  • digital PCR (copy number variation, SNP or absolute quantification)
  • Single cell expression profiling
  • Library preparation, quality control and experimental design of RNA-Seq
  • miRNA analysis (Two-Tailed RT-qPCR – design and validation)
  • Elementary data analysis


  • CFX96 // BioRad // qPCR
  • CFX384 // BioRad // qPCR
  • LightCycler 480 II // Roche // qPCR
  • QX200 // Biorad // dPCR
  • Biomark // Fluidigm // high-throughput qPCR
  • EpMotion P5073 // Eppendorf // pipetting robot
  • Fragment Analyzer // Agilent // capillary electrophoresis for QC of nucleic acids
  • CellCelector™// ALS // automated single cell and colony picking system
  • NanoDrop 8000 // Thermo Fisher Scientific // spectrophotometer
  • Chromium Controller // 10x Genomics // Library preparation for single cells

!! The course on September 25-27 has been canceled, new date will be announced as soon as possible!!

We apologize for any inconvenience and look forward to seeing you at an alternative date.

3-days Basic practical qPCR course, September 25-27, 2023

Quantitative polymerase chain reaction (qPCR) is a vital tool in scientific research due to its ability to accurately measure and analyse DNA or RNA samples. It enables precise quantification of gene expression levels, providing valuable insights into biological processes and disease mechanisms.

The Gene Core facility, in close collaboration with the Laboratory of Gene Expression, is hosting a comprehensive 3-day Basic Practical qPCR Course. GeneCore is a specialized service provider that focuses on gene expression analysis and its application in various experiments. With nearly 15 years of experience in lecturing on qPCR courses, as well as offering comprehensive training in Single Cell Analysis, miRNA Analysis, Digital PCR, and NGS Library Preparation, we have developed a strong expertise in molecular biology education and practical laboratory techniques.

Course schedule:

1.Day: Introduction to qPCR, Experimental design, Assay design, 1st Experiment

2.Day: Normalization and Quantification, Assays validation, 2nd Experiment

3.Day: Sample preparation and QC, Reverse transcription, MIQE guidelines, 3rd Experiment


Date: September 25-27, 2023Obrázek1

Venue: BIOCEV campus, Průmyslová 595, 252 50 Vestec

Online registration form: link

Maximum capacity: 12 people

Registration deadline: August 21, 2023

Course fee: 15 000 CZK, VAT excluded

Please do not hesitate to contact us for a group discount.

Lunch, snacks and coffee are included in the course fee. Printed course materials are included in the course fee. The course fee does not include accommodation, breakfast, dinner or travel expenses.

Terms and Conditions (CZ and EN version)

For more information please contact us at or (+420) 325 873 746.