Laboratory of Single Cell Analyses

Dr. habil. Paulina Jackowiak , Assoc. Prof.

Head of Laboratory

paulinaj@ibch.poznan.pl
ext. 1640
mail of laboratory: labsinglecell@ibch.poznan.pl

Research Projects

Keywords

single cell RNA-Seq
single cell ATAC-Seq
multiomics
flow cytometry
cell sorting
high-throughput imaging

Offer

We integrate experimental and computational approaches to comprehensively characterize diverse biological material at single cell resolution.

The infrastructure of the Laboratory is part of a platform for multidimensional imaging of biological processes, established within the framework of NEBI - National Research Center for Imaging in the Biological and Biomedical Sciences. The Laboratory is included in one of the centers of the LifeTime consortium (https://lifetime-initiative.eu), co-founded by the Institute of Bioorganic Chemistry, PAS.

We offer gene expression and chromatin accessibility profiling, as well as cell sorting and advanced analyses using classical and imaging flow cytometry. We provide equipment for quantitative and qualitative analysis of nucleic acids.

We welcome collaborations on projects including the study of heterogeneous or rare cell populations, detection of extracellular vesicles, or visualization of intracellular processes and interactions.

Info

Info for IBCH PAS – click here

Equipment

pdf brochure - download

Chromium Controller (10x Genomics)
Chromium X (10x Genomics)
Drop-Seq (Fluigent)
Amnis ImageStreamX Mk II imaging flow cytometer (Cytek Biosciences), in 405/488/561/642 nm laser configuration
FACSAria Fusion cell sorter (Becton Dickinson), in 405/488/561/640 nm laser configuration, with Automated Cell Deposition Unit (ACDU) for directly sorting onto multiwell plates and microscope slides
Guava easyCyte 12HT flow cytometer (Cytek Biosciences), in 405/488/642 nm laser configuration
Guava Muse Cell Analyzer (Cytek Biosciences)
QX200 Droplet Digital PCR system (BioRad)
CFX96 Real-time PCR system (BioRad)
BluePippin DNA fractionator (Sage Science)
TapeStation 4150 nucleic acid analyzer (Agilent)
Laminar flow cabinet (BioTectum)
CB 170 CO2 incubator (Binder)
gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec)
Minilys homogenizer (Bertin Instrument)
McIlwain Tissue Chopper
EVE automated cell counter (NanoEnTek)
Countess 3 FL automated cell counter (Invitrogen)
Qubit 4 fluorimeter (Invitrogen)
T-100 thermal cycler (BioRad)
VeritiPro thermal cycler (Applied Biosystems)
epMotion 5073t liquid handler (Eppendorf)
on-premise high performance computer
access to a supercomputing cluster

Grants

INTERCEPT – Targeted single-cell technology for cancer diagnostics – towards cell-oriented interceptive medicine (UoF/02-WIB-3/2023-004). The project is funded under the Virtual Research Institute Programme from the Polish Science Fund.
European Center for Bioinformatics and Genomics – MOSAIC 3D (FENG.02.04-IP.04-0012/24). The project is co-funded through European Funds for Smart Economy 2021-2027 Programme (FENG), Action 2.4 Smart Economy Research Infrastructure.
Comprehensive analysis of the Schmidtea mediterranea transcriptome – identification of non-coding RNAs involved in cell lineage development during regeneration (2019/35/B/NZ2/02658). NCN OPUS 18

Selected publications

Dutta, A.; Zaremba, A.; Jackowiak, P. Ribonucleases in Mendelian disease: Characterization and insight from model organisms. Genes Dis, 2025, 12 (5): 101613.
Kulak, K.; Samelak-Czajka, A.; Marszalek-Zenczak, M.; Michalak, K. M.; Trybus, M.; Minicka, J.; Jackowiak, P.; Bagniewska-Zadworna, A. Identification of phloem-specific proteinaSEOus structure heterogeneity in sieve element of Populus trichocarpa. BMC Plant Biol, 2025, 25 (1): 456.
Szostak, N.; Budnik, M.; Tomela, K.; Handschuh, L.; Samelak-Czajka, A.; Pietrzak, B.; Schmidt, M.; Kaczmarek, M.; Galus, L.; Mackiewicz, J.; Mackiewicz, A.; Kozlowski, P.; Philips, A. Exploring correlations between gut mycobiome and lymphocytes in melanoma patients undergoing anti-PD-1 therapy. Cancer Immunol Immunother, 2025, 74 (4): 110.
Zimmer, K.; Chmielewska, A. M.; Jackowiak, P.; Figlerowicz, M.; Bienkowska-Szewczyk, K. Alterations in N-glycosylation of HCV E2 Protein in Children Patients with IFN-RBV Therapy Failure. Pathogens, 2024, 13 (3).
Bartelt, L. C.; Fakhri, M.; Adamek, G.; Trybus, M.; Samelak-Czajka, A.; Jackowiak, P.; Fiszer, A.; Lowe, C. B.; La Spada, A. R.; Switonski, P. M. Antibody-assisted selective isolation of Purkinje cell nuclei from mouse cerebellar tissue. Cell Rep Methods, 2024, 4 (7): 100816.
Baliga-Gil, A.; Soszynska-Jozwiak, M.; Ruszkowska, A.; Szczesniak, I.; Kierzek, R.; Ciechanowska, M.; Trybus, M.; Jackowiak, P.; Peterson, J. M.; Moss, W. N.; Kierzek, E. Targeting sgRNA N secondary structure as a way of inhibiting SARS-CoV-2 replication. Antiviral Res, 2024, 228: 105946.
Szostak, N.; Handschuh, L.; Samelak-Czajka, A.; Tomela, K.; Pietrzak, B.; Schmidt, M.; Galus, L.; Mackiewicz, J.; Mackiewicz, A.; Kozlowski, P.; Philips, A. Gut Mycobiota Dysbiosis Is Associated with Melanoma and Response to Anti-PD-1 Therapy. Cancer Immunol Res, 2024, 12 (4): 427-439.
Mieloch, A. A.; Mleczko, A. M.; Samelak-Czajka, A.; Jackowiak, P.; Rybka, J. D. Biomimetic virus-like particles with magnetic core. From bioactivity to an immunodiagnostic tool. Chem Eng J, 2024, 485.
Kulak, K.; Wojciechowska, N.; Samelak-Czajka, A.; Jackowiak, P.; Bagniewska-Zadworna, A. How to explore what is hidden? A review of techniques for vascular tissue expression profile analysis. Plant Methods, 2023, 19 (1): 129.
Budzko, L.; Hoffa-Sobiech, K.; Jackowiak, P.; Figlerowicz, M. Engineered deaminases as a key component of DNA and RNA editing tools. Mol Ther Nucleic Acids, 2023, 34.
Samelak-Czajka, A.; Wojciechowski, P.; Marszalek-Zenczak, M.; Figlerowicz, M.; Zmienko, A. Differences in the intraspecies copy number variation of Arabidopsis thaliana conserved and nonconserved miRNA genes. Funct Integr Genomics, 2023, 23 (2): 120.
Stolarek, I.; Samelak-Czajka, A.; Figlerowicz, M.; Jackowiak, P. Dimensionality reduction by UMAP for visualizing and aiding in classification of imaging flow cytometry data. iScience, 2022, 25 (10): 105142.
Strybel, U.; Marczak, L.; Zeman, M.; Polanski, K.; Mielanczyk, L.; Klymenko, O.; Samelak-Czajka, A.; Jackowiak, P.; Smolarz, M.; Chekan, M.; Zembala-Nozynska, E.; Widlak, P.; Pietrowska, M.; Wojakowska, A. Molecular Composition of Serum Exosomes Could Discriminate Rectal Cancer Patients with Different Responses to Neoadjuvant Radiotherapy. Cancers (Basel), 2022, 14 (4).
Rajewsky, N.; Almouzni, G.; Gorski, S. A.; Aerts, S.; Amit, I.; Bertero, M. G.; Bock, C.; Bredenoord, A. L.; Cavalli, G.; Chiocca, S.; Clevers, H.; De Strooper, B.; Eggert, A.; Ellenberg, J.; Fernandez, X. M.; Figlerowicz, M.; Gasser, S. M.; Hubner, N.; Kjems, J.; Knoblich, J. A.; Krabbe, G.; Lichter, P.; Linnarsson, S.; Marine, J. C.; Marioni, J. C.; Marti-Renom, M. A.; Netea, M. G.; Nickel, D.; Nollmann, M.; Novak, H. R.; Parkinson, H.; Piccolo, S.; Pinheiro, I.; Pombo, A.; Popp, C.; Reik, W.; Roman-Roman, S.; Rosenstiel, P.; Schultze, J. L.; Stegle, O.; Tanay, A.; Testa, G.; Thanos, D.; Theis, F. J.; Torres-Padilla, M. E.; Valencia, A.; Vallot, C.; van Oudenaarden, A.; Vidal, M.; Voet, T.; LifeTime Community Working Groups (inc. Jackowiak, P., Koralewska, N.). LifeTime and improving European healthcare through cell-based interceptive medicine. Nature, 2020, 587 (7834): 377-386.
Jackowiak, P.; Hojka-Osinska, A.; Philips, A.; Zmienko, A.; Budzko, L.; Maillard, P.; Budkowska, A.; Figlerowicz, M. Small RNA fragments derived from multiple RNA classes - the missing element of multi-omics characteristics of the hepatitis C virus cell culture model. BMC Genomics, 2017, 18 (1): 502.

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