GeneCore

GeneCore, located within the Institute of Biotechnology at the Czech Academy of Sciences, is a top facility dedicated to providing cutting-edge transcriptomic services. With over 18 years of experience in the field, we specialize in single-cell and spatial transcriptomics, offering comprehensive support from experimental design to data analysis.

Our Expertise

At GeneCore, we are committed to empowering researchers with advanced techniques for transcriptomic analysis. Our state-of-the-art laboratory is equipped with cutting-edge technology, allowing us to design experiments for wide range of research objectives.

Single-Cell Profiling

With our expertise in single-cell profiling, we enable researchers to explore cellular diversity, heterogeneity, and gene expression patterns at the individual cell level. Through meticulous sample quality control and validated library preparation, we deliver accurate and reliable results, ensuring high-quality data for your research needs.

Spatial Transcriptomics

Moreover, our facility boasts advanced spatial transcriptomic technology, allowing researchers to visualize gene expression within intact tissue samples. By unraveling the spatial organization of cellular activity, we provide invaluable insights into tissue architecture and function.

Our Mission

GeneCore Facility's primary goal is to support groundbreaking researchs within the Institute of Biotechnology at the Czech Academy of Sciences and beyond. We collaborate closely with leading scientists and leverage the latest transcriptomic platforms to deliver exceptional services in single-cell and spatial transcriptomics.

Supporting Research Excellence

In alignment with the mission and vision of the Institute of Biotechnology at the Czech Academy of Sciences, our services contribute to diverse research initiatives aimed at unraveling biomolecular mechanisms. By facilitating a deeper understanding of complex diseases and cellular dynamics, we pave the way for the development of next-generation medicines and innovative biotechnologies.

Get in Touch

Partner with GeneCore Facility today to unlock the full potential of transcriptomic analysis and accelerate your research journey. Contact us to discuss your project requirements and discover how our expertise can drive scientific discovery and innovation.

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.

scRT-qPCR

• 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.

Our services encompass the complete experimental workflow, comprising experimental design, sample preparation and quality control, library preparation, RNA-sequencing, and data analysis. These services are available to internal users, academic users, and external commercial users. Prices are provided in CZK without VAT, with detailed quotations available upon request. For inquiries, please contact Eva Rohlová - eva.rohlova@ibt.cas.cz.

Bulk Transcriptomics

Method Description: Bulk RNA-sequencing analyzes the complete transcriptome in a tissue or cell culture sample.

Validated library preparation kits: QuantSeq 3’ mRNA-Seq V2 Library Prep Kit from Lexogen (link); SureSelect XT HS2 mRNA Library Preparation Kit (link); NEBNext® Ultra™ II Directional RNA Library Prep Kit (link); NEBNext® Single Cell/Low Input RNA Library Prep Kit (link); RealSeq®-AC and RealSeq®-Biofluids (link).

Sample Input: Tissues, Cell Pellets, RNA sample of sufficient quality.

Output: Pool of libraries ready for sequencing.

Delivery Time: 2-3 weeks.

Informative Price: From 1 500 CZK per sample.*

Single-Cell Transcriptomics by 10x Genomics

Method Description: A widely utilized method for single-cell multiomics with versatile applications (link).

Sample Input: Dissociated fresh or fixed cells of sufficient quantity and quality (typically > 100k cells) or piece of tissue for analysis of nuclei.

Output: Pool of libraries ready for sequencing.

Delivery Time: 2-3 weeks.

Informative Price: From 40 000 CZK per sample.*

Single-Cell Transcriptomics by ParseBiosciences

Method Description: Combinatorial barcoding technology with high multiplexing capacity (link).

Sample Input: Dissociated fresh or fixed cells of sufficient quantity and quality (typically > 200k cells) or piece of tissue for analysis of nuclei.

Output: Pool of libraries ready for sequencing.

Delivery Time: 2-3 weeks.

Informative Price: From 10 000 CZK per sample.*

Single-Cell Transcriptomics by FluentBiosciences

Method Description: Scalable and cost-effective technology with a high recovery rate (link).

Sample Input: Dissociated fresh cells of sufficient quality (from 10k cells).

Output: Pool of libraries ready for sequencing.

Delivery Time: 2-3 weeks.

Informative Price: From 10 000 CZK per sample.*

Plate-based Single-Cell Transcriptomics (Smart-seq3xpress)

Method Description: Plate-based full-length single-cell library preparation method based on Smart-seq3xpress protocol (link)

Sample Input: Individual cells or mini-bulks collected in a 384-well plate.

Output: Pool of libraries ready for sequencing.

Delivery Time: 2-3 weeks.

Informative Price: From 15 000 CZK per 384-well plate.

Spatial Transcriptomics by 10x Genomics

Method Description: A widely utilized method for spatial transcriptomics with versatile applications (link).

Sample Input: Fresh frozen or formalin‐fixed paraffin‐embedded tissues or slices.

Output: Pool of libraries ready for sequencing.

Delivery Time: 2-3 weeks.

Informative Price: From 50 000 CZK per sample.*

Sequencing Services

Method Description: NovaSeqX platform (link)**.

Input: Pool of libraries.

Output: Raw sequencing files.

Delivery time: Upon inquiry.

Informative Price: Upon inquiry.

Data Analysis

Method Description: Basic data analysis for bulk as well as single-cell transcriptomics.

Input: Raw sequencing files.

Output: Analysis report summarizing quality metrics, descriptive statistics, and key findings. Advanced analysis upon inquiry.

Delivery time: Upon inquiry.

Informative Price: Upon inquiry.

List of Additional Services:

 Consultation and experimental design

Method selection, sample collection, quality control tools, pilot experiment, data analysis options

Sample preparation, processing and quality control

RNA extraction, assessment of RNA quality and quantity, RT-qPCR-based quality control, cell viability assessment and cell counting

Reverse transcription quantitative PCR

Assay design and validation, quality control assays, bulk and single-cell RNA profiling, high-throughput mRNA profiling (BioMark platform), miRNA profiling (Two-tailed RT-PCR), Data analysis

 Digital droplet PCR

 * Estimated price depends on the number of samples and varies 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