Laboratory of Single Cell Analyses

Dr. hab. Paulina Jackowiak, prof. IBCH PAS

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 Imaging Centre for 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

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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

Research activity

POIR.04.02.00-00-D017/20 European Centre for Bioinformatics and Genomics – MOSAIC
POIR.04.02.00-00-C004/19 NEBI – National Imaging Centre for biological and biomedical sciences
Both projects are co-financed through the European Regional Development Fund (ERDF) in the frame of Smart Growth Operational Programme 2014-2020 (Measure 4.2 Development of modern research infrastructure of the science sector).
2019/35/B/NZ2/02658 Comprehensive analysis of the Schmidtea mediterranea transcriptome – identification of non-coding RNAs involved in cell lineage development during regeneration. NCN OPUS 18

Selected publications

Mieloch, A.; Mleczko, A.; Samelak-Czajka, A.; Jackowiak, P.; Rybka, J. Biomimetic virus-like particles with magnetic core. From bioactivity to an immunodiagnostic tool. Chemical Engineering Journal, 2024, 485: 149714.
Szostak, N.; Handschuh, L.; Samelak-Czajka, A.; Tomela, K.; Pietrzak, B.; Schmidt, M.; Galus, Ł.; 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, OF1–OF13.
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), 256.
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: 102062.
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.
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.
Szostak, N.; Handschuh, L.; Samelak-Czajka, A.; Tomela, K.; Schmidt, M.; Pruss, L.; Milanowska-Zabel, K.; Kozlowski, P.; Philips, A. Host Factors Associated with Gut Mycobiome Structure. mSystems, 2023: e0098622.
Marszalek-Zenczak, M.; Satyr, A.; Wojciechowski, P.; Zenczak, M.; Sobieszczanska, P.; Brzezinski, K.; Iefimenko, T.; Figlerowicz, M.; Zmienko, A. Analysis of Arabidopsis non-reference accessions reveals high diversity of metabolic gene clusters and discovers new candidate cluster members. Front Plant Sci, 2023, 14: 1104303.
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.
Szostak, N.; Szymanek, A.; Havranek, J.; Tomela, K.; Rakoczy, M.; Samelak-Czajka, A.; Schmidt, M.; Figlerowicz, M.; Majta, J.; Milanowska-Zabel, K.; Handschuh, L.; Philips, A. The standardisation of the approach to metagenomic human gut analysis: from sample collection to microbiome profiling. Sci Rep, 2022, 12 (1): 8470.
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).
Butkiewicz, D.; Krzesniak, M.; Gdowicz-Klosok, A.; Giglok, M.; Marszalek-Zenczak, M.; Suwinski, R. Polymorphisms in EGFR Gene Predict Clinical Outcome in Unresectable Non-Small Cell Lung Cancer Treated with Radiotherapy and Platinum-Based Chemoradiotherapy. Int J Mol Sci, 2021, 22 (11): 5605.
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.
Zmienko, A.; Marszalek-Zenczak, M.; Wojciechowski, P.; Samelak-Czajka, A.; Luczak, M.; Kozlowski, P.; Karlowski, W. M.; Figlerowicz, M. AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome. Plant Cell, 2020, 32 (6): 1797-1819.
Jackowiak, P.; Lis, A.; Luczak, M.; Stolarek, I.; Figlerowicz, M. Functional characterization of RNA fragments using high-throughput interactome screening. J Proteomics, 2019, 193: 173-183.

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