GeneCore Facility

GeneCore Facility

Ing. Lukáš Valihrach, Ph.D.

Ing. Lukáš Valihrach, Ph.D. — Laboratory head

About us

The GeneCore Facility offers advanced transcriptomic services for both academic and commercial users, specializing in bulk, single-cell, and spatial transcriptomics. We support the entire experimental workflow, including experimental design, sample preparation and quality control, library preparation, sequencing, and comprehensive data analysis services.

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.

 

News

Services

GeneCore Facility is a leading research laboratory providing cutting-edge transcriptomic services. 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.*

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.

Publications

2015

Pre-amplification in the context of high-throughput qPCR gene expression experiment. Korenková V, Scott J, Novosadová V, Jindřichová M, Langerová L, Švec D, Šídová M, Sjöback R. BMC Mol Biol. 2015 Mar 11;16:5. doi: 10.1186/s12867-015-0033-9.

Post-treatment recovery of suboptimal DNA repair capacity and gene expression levels in colorectal cancer patients. Slyskova J, Cordero F, Pardini B, Korenkova V, Vymetalkova V, Bielik L, Vodickova L, Pitule P, Liska V, Matejka VM, Levy M, Buchler T, Kubista M, Naccarati A, Vodicka P. Mol Carcinog. 2015 Sep;54(9):769-78. doi: 10.1002/mc.22141. Epub 2014 Mar 3

2014

SPIDIA-RNA: second external quality assessment for the pre-analytical phase of blood samples used for RNA based analyses. Malentacchi F, Pazzagli M, Simi L, Orlando C, Wyrich R, Günther K, Verderio P, Pizzamiglio S, Ciniselli CM, Zhang H, Korenková V, Rainen L, Bar T, Kubista M, Gelmini S. PLoS One. 2014 Nov 10;9(11):e112293. doi: 10.1371/journal.pone.0112293. eCollection 2014.

Biomarkers for monitoring pre-analytical quality variation of mRNA in blood samples. Zhang H, Korenková V, Sjöback R, Švec D, Björkman J, Kruhøffer M, Verderio P, Pizzamiglio S, Ciniselli CM, Wyrich R, Oelmueller U, Kubista M, Lindahl T, Lönneborg A, Rian E. PLoS One. 2014 Nov 4;9(11):e111644. doi: 10.1371/journal.pone.0111644. eCollection 2014.

Molecular characteristics of mismatch repair genes in sporadic colorectal tumors in Czech patients. Vymetalkova VP, Slyskova J, Korenkova V, Bielik L, Langerova L, Prochazka P, Rejhova A, Schwarzova L, Pardini B, Naccarati A, Vodicka P. BMC Med Genet. 2014 Jan 31;15:17. doi: 10.1186/1471-2350-15-17.

Effect of zearalenone on reproductive parameters and expression of selected testicular genes in mice. Zatecka E, Ded L, Elzeinova F, Kubatova A, Dorosh A, Margaryan H, Dostalova P, Korenkova V, Hoskova K, Peknicova J. Reprod Toxicol. 2014 Jun;45:20-30. doi: 10.1016/j.reprotox.2014.01.003. Epub 2014 Jan 9.

2013

Evaluation of tumor suppressor gene expressions and aberrant methylation in the colon of cancer-induced rats: a pilot study. Polakova Vymetalkova V, Vannucci L, Korenkova V, Prochazka P, Slyskova J, Vodickova L, Rusnakova V, Bielik L, Burocziova M, Rossmann P, Vodicka P. Mol Biol Rep. 2013 Oct;40(10):5921-9. doi: 10.1007/s11033-013-2699-8. Epub 2013 Sep 25.

Association of obesity susceptibility gene variants with metabolic syndrome and related traits in 1,443 Czech adolescents. Dušátková L, Zamrazilová H, Sedláčková B, Včelák J, Hlavatý P, Aldhoon Hainerová I, Korenková V, Bradnová O, Bendlová B, Kunešová M, Hainer V. Folia Biol (Praha). 2013;59(3):123-33.

Microfluidic high-throughput RT-qPCR measurements of the immune response of primary bovine mammary epithelial cells cultured from milk to mastitis pathogens. Sorg D, Danowski K, Korenkova V, Rusnakova V, Küffner R, Zimmer R, Meyer HH, Kliem H. Animal. 2013 May;7(5):799-805. doi: 10.1017/S1751731112002315. Epub 2012 Dec 11.