Facilities

Dr hab. Marta Koblowska

Microarray Analysis Facility

ORCID: 0000-0003-4497-6200

E-mail:

Service and research scope

The Microarray Analysis Facility, founded in 2008, provides an extensive range of microarray-based services to researchers in the academic, pharmaceutical and commercial sectors.

The team members are highly experienced in the field of basic research and not only perform microarrays analysis with highest standards, but also offer consulting in experimental design, assay performance, as well as data analysis and interpretation.

Our laboratory has comprehensive experience in gene expression profiling and DNA methylation analysis using microarray technology.

Additionally, our Facility offers RNA/DNA quality analysis and qPCR of DNA and RNA samples.

Kontakt

Roksana Iwanicka-Nowicka (PhD, DSc), email: roxana@ibb.waw.pl, phone: +48 22 592 24 12

Marta Koblowska (PhD, DSc), email: marta@ibb.waw.pl, phone: +48 22 592 24 12

Service

Service Description

Gene Expression Analysis

Expression Profiling using Thermo Fisher (previously Affymetrix) microarrays.

The Facility of Microarray Analysis offers expression analysis services including Whole Transcript (WT) Expression arrays ( Clariom D arrays, Clariom S arrays, gene arrays), 3′ Expression arrays and miRNA arrays.  Submitted for expression analysis RNA samples undergoes a mandatory quality and quantity assessment using the Agilent Bioanalyzer.

For the analysis of human, rat and mouse transcriptome at the gene-level detection our Facility recommends using Clariom S and for both the gene-level and the identification of known transcript isoforms we recommend Clariom D assays. These assays provide a substantial amount of information at a favorable cost.

Clariom D arrays:

  • offer an exceptionally in-depth analysis of the transcriptome, examining over 540 000 transcripts, providing the fastest route to actionable results from as little as 100 pg of total RNA
  • enable translational research specialists to quickly and easily create highly accurate biomarker profiles
  • provide highly sophisticated understanding of gene and exon expression at the transcriptome level, including the capability to detect alternative splicing events in both coding and long non-coding (lnc) RNA, all within a single three-day experiment
  • stands as the most comprehensive among whole-transcript expression arrays, specializing in profiling the transcriptomes of humans, mice, and rats
  • offers the necessary coverage and precision required for identifying all known transcript isoforms originating from a single gene.

The Clariom S assay offers a targeted analysis of gene-level expression within a transcriptome focused on 20,000 best-annotated genes, making them suitable for various clinical sample types. Clariom S Assays are the preferred tools for efficiently and affordably discovering expression biomarkers with well-defined functions.

Clariom S and Clariom D assays:

  • Create reliable expression profiles from just 100 pg of total RNA
  • Utilize total RNA from diverse sample sources such as whole blood, cultured cells and fresh/fresh-frozen or formalin fixed, paraffin-embedded (FFPE) tissues
  • Maintain sample integrity and minimize data fluctuations using an assay not requiring a globin or rRNA removal.

 

Epigenetics

DNA methylation profiling at the single-CpG-site level using Illumina Infinium MethylationEPIC BeadChips.

The Facility of Microarray Analysis offers Illumina methylation BeadArray technology.

Aberrant DNA methylation pattern results in the deregulation of gene expression and has been implicated in numerous cancers. With the Illumina Human MethylationEPIC Array you can not only perform epigenome-wide association studies but also identify differentially methylated sites in tumor versus normal tissues.

Now available the newest Infinium MethylationEPIC v2.0 Array – an enhanced version of the EPIC v1.0 representing Illumina’s state-of-the-art approach for genome-wide DNA methylation analysis, leveraging bisulfite conversion. This advanced technique facilitates the precise quantification of the overall methylation status at more than 930,000 individual methylation sites across the human genome, down to single nucleotide resolution. It provides extensive coverage of critical regions in the methylome, including CpG islands, enhancer regions, open chromatin sites, and other significant genomic areas, featuring expanded content in comparison to the EPIC v1.0.

Infinium MethylationEPIC v2.0 Array covers the following content areas:

  • Expanded coverage of CpG islands
  • Enhanced exon coverage for more accurate copy number variation (CNV) detection
  • Non-CpG (CHH) methylated sites identified in human stem cells sites
  • ENCODE open chromatin and enhancers
  • FANTOM5 enhancers
  • DNase hypersensitivity sites
  • miRNA promoter regions
  • Enhancers and super-enhancers identified by ChIP-Seq in cancer and cell line samples Differentially methylated sites identified in tumor versus normal samples for multiple cancers
  • Differentially accessible chromatin regions identified in primary human cancers using ATAC-Seq
  • Common cancer driver mutations
  • > 85% HumanMethylation450 BeadChip content

 

RNA/DNA analysis using Bioanalyzer

Quality and quantity verification of RNA or DNA samples for any downstream application, analysis using Agilent Bioanalyzer is available.

 

qPCR analysis

The Facility of Microarray Analysis offers Realtime PCR analysis, both qualitative and quantitative of DNA and RNA samples, using Roche LightCycler 480 Instrument.
The service offered includes primer design for selected matrices, optimization of the assay, verification of RNA purity, if applicable, and Realtime PCR analysis. Preliminary quantitative analysis of the data is also available.

Equipment

GeneChip®Scanner 3000 Targeted Genotyping System (Affymetrix) including the GeneChip Scanner 3000 7G with AutoLoader, two Fluidics Stations 450, Hybridization Oven 645 and Affymetrix GeneChip Command Console Software (AGCC). This system enables transcriptomic analysis using Clariom S and Clariom D arrays, interrogation of miRNA composition with dedicated GeneChip arrays as well as High Resolution Chromosome Copy Number Analysis Using GeneChip Mapping Arrays.

The HiScanSQ system (Illumina) facilitated epigenetic analysis with Infinium MethylationEPIC v2.0 Array

LightCycler-480 Roche – a high-performance PCR platform that delivers methods for gene detection, gene expression analysis, genetic variation analysis and array data validation.

Bioruptor® Plus sonication device (Diagenode) used for chromatin fragmentation, a preliminary and necessary step to obtain starting material for preparing libraries for analysis using ChiP-seq next-generation sequencing.

2100 Bioanalyzer (Agilent) used for the control of quality nucleic acids samples. It uses capillary electrophoresis technique and allows up to 12 samples to be analyzed in parallel. The device allows to evaluate the quality of both DNA and RNA, before and during the microarray analysis steps, as well as to assess the quality of the performed libraries for next-generation sequencing.

The NanoDrop ND-1000 spectrophotometer allows measuring the absorbance of nucleic acids in 1 µl volume, with high accuracy and reproducibility, over a wide range of concentrations (2-3700 ng/ µl for double-stranded DNA).

MagNa Lyser Instrument (Roche Diagnostics) a homogenization module allows automated fragmentation of tissues and consequent disintegration of cells of various origins.

MagNA Pure Compact Instrument (Roche Diagnostics) enables isolation of DNA or RNA simultaneously from eight samples and provides guarantees of safety in working with human material and excludes the possibility of contamination of samples, while ensuring high reproducibility of isolation performance.

Collaborations

  • Prof. dr hab. Agnieszka Piekiełko-Witkowska,, Centre of Postgraduate Medical Education, Warsaw, Poland

  • Dr hab. Joanna Bogusławska, prof. CMKP, Centre of Postgraduate Medical Education, Warsaw, Poland

  • Prof. dr hab. Maria Anna Ciemerych-Litwinienko, Faculty of Biology, University of Warsaw, Poland

  • Dr hab. Edyta Brzósko-Wójtowicz, prof. ucz , Faculty of Biology, University of Warsaw, Poland

  • Dr hab. Renata Matlakowska, prof. ucz, Faculty of Biology, University of Warsaw, Poland

  • Dr n. med. Łukasz Szafron, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland

  • Dr hab. n. med. Tomasz Mazurek, First Chair and Department of Cardiology, Medical University of Warsaw, Warsaw, Poland

  • Prof. dr hab. Agnieszka Chacińska IMol PAS, Warsaw, Poland

  • Dr hab. Anna Żmijewska-Bielak, prof. inst, Nencki Institute of Experimental Biology PAS, Warsaw, Poland

Customers

  • Centre of Molecular and Macromolecular Studies PAS, Łódź , Poland

  • University of Warsaw, Poland

  • Institute of Animal Reproduction and Food Research PAS, Olsztyn , Poland

  • Medical University of Lodz, Łódź, Poland

  • University of Wrocław, Wrocław, Poland

  • The Institute of Medical Biology PAS, Łódź, Poland

  • Gdańsk University of Technology, Gdańsk, Poland.

  • Centre of Postgraduate Medical Education, Warsaw, Poland

  • University of Life Sciences-SGGW, Warsaw, Poland.

  • Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland

  • Medical University of Warsaw, Warsaw, Poland

  • Nencki Institute of Experimental Biology PAS, Warsaw, Poland

  • Institute of Genetics and Animal Biotechnology, PAS, Jastrzębiec, Poland

  • Institute of Psychiatry and Neurology, Warsaw, Poland

  • Medical University of Gdańsk, Gdańsk, Poland

  • Adamed

  • Biomedica

  • Openexom

Research

Research Description

The Facility of Microarray Analysis has participated in numerous studies that cover different organisms and cell types, utilizing DNA microarrays. Our involvement in transcriptomic analysis spans experiment planning, executing microarray experiments, and conducting bioinformatics analysis.

Selected Publications

  • Coordinated reprogramming of renal cancer transcriptome, metabolome and secretome associates with immune tumor infiltration. Poplawski P, Alseekh S, Jankowska U, Skupien-Rabian B, Iwanicka-Nowicka R, Kossowska H, Fogtman A, Rybicka B, Bogusławska J, Adamiok-Ostrowska A, Hanusek K, Hanusek J, Koblowska M, Fernie AR, Piekiełko-Witkowska A. Cancer Cell Int. 2023 Jan 5;23(1):2. doi: 10.1186/s12935-022-02845-y.
  • The miR151 and miR5100 Transfected Bone Marrow Stromal Cells Increase Myoblast Fusion in IGFBP2 Dependent Manner. Mierzejewski B, Michalska Z, Jackowski D, Streminska W, Janczyk-Ilach K, Koblowska M, Iwanicka-Nowicka R, Gromadka A, Ciemerych MA, Brzoska E. Stem Cell Rev Rep. 2022 Aug;18(6):2164-2178. doi: 10.1007/s12015-022-10350-y. Epub 2022 Feb 21. PMID: 35190967; PMCID: PMC9391248.
  • Gene expression profile in patients with Gaucher disease indicates activation of inflammatory processes. Ługowska A, Hetmańczyk-Sawicka K, Iwanicka-Nowicka R, Fogtman A, Cieśla J, Purzycka-Olewiecka JK, Sitarska D, Płoski R, Filocamo M, Lualdi S, Bednarska-Makaruk M, Koblowska M.. Sci Rep. 2019 Apr 15;9(1):6060. doi: 10.1038/s41598-019-42584-1.
  • HD2C histone deacetylase and a SWI/SNF chromatin remodelling complex interact and both are involved in mediating the heat stress response in Arabidopsis. Buszewicz D, Archacki R, Palusiński A, Kotliński M, Fogtman A, Iwanicka-Nowicka R, Sosnowska K, Kuciński J, Pupel P, Olędzki J, Dadlez M, Misicka A, Jerzmanowski A, Koblowska MK. Plant Cell Environ. 2016 Oct;39(10):2108-22. doi: 10.1111/pce.12756.
  • Mistargeted mitochondrial proteins activate a proteostatic response in the cytosol. Wrobel L, Topf U, Bragoszewski P, Wiese S, Sztolsztener ME, Oeljeklaus S, Varabyova A, Lirski M, Chroscicki P, Mroczek S, Januszewicz E, Dziembowski A, Koblowska M, Warscheid B, Chacinska A. Nature. 2015 Aug 27;524(7566):485-8. doi: 10.1038/nature14951.

Publications (IBB PAS affiliated)

SZAFRON L.A., IWANICKA-NOWICKA R., SOBICZEWSKI P., KOBLOWSKA M., DANSONKA-MIESZKOWSKA A., KUPRYJANCZYK J., SZAFRON Ł., The diversity of methylation patterns in serous borderline ovarian tumors and serous ovarian carcinomas. Cancers (2024) 16(20): 3524 (27 p.) DOI: 10.3390/cancers16203524 IF 4.5 (2023)
SZAFRON L.A., IWANICKA-NOWICKA R., PODGÓRSKA A., BONNA A., SOBICZEWSKI P., KUPRYJANCZYK J., SZAFRON Ł., The clinical significance of CRNDE gene methylation, polymorphisms, and CRNDEP micropeptide expression in ovarian tumors. International Journal of Molecular Sciences (2024) 25(14): 7531 (23 p.) DOI: 10.3390/ijms25147531 IF 4.9 (2023)
POPŁAWSKI P., ZARYCHTA-WIŚNIEWSKA W., BURDZIŃSKA A., BOGUSŁAWSKA J., ADAMIOK-OSTROWSKA A., HANUSEK K., RYBICKA B., BIAŁAS A., KOSSOWSKA H., IWANICKA-NOWICKA R., KOBLOWSKA M., PĄCZEK L., PIEKIEŁKO-WITKOWSKA A. Renal cancer secretome induces migration of mesenchymal stromal cells. Stem Cell Research & Therapy (2023) 14(1): 200 (13 p.) DOI: 10.1186/s13287-023-03430-4 IF 7.1 (2023)
MIERZEJEWSKI B., GRABOWSKA I., MICHALSKA Z., ZDUŃCZYK K., ZARĘBA F., IRHASHAVA A., CHRZĄSZCZ M., PATRYCY M., STREMIŃSKA W., JAŃCZYK-ILACH K., KOBLOWSKA M., IWANICKA-NOWICKA R., GROMADKA A., KOWALSKI K., CIEMERYCH M.A., BRZÓSKA E., SDF-1 and NOTCH signaling in myogenic cell differentiation: the role of miRNA10a, 425, and 5100. Stem Cell Research & Therapy (2023) 14(1): 204 (26 p.) DOI: 10.1186/s13287-023-03429-x IF 7.1 (2023)
POPŁAWSKI P., ALSEEKH S., JANKOWSKA U., SKUPIEŃ-RABIAN B., IWANICKA-NOWICKA R., KOSSOWSKA H., FOGTMAN A., RYBICKA B., BOGUSŁAWSKA J., ADAMIOK-OSTROWSKA A., HANUSEK K., HANUSEK J., KOBLOWSKA M., FERNIE A.R., PIEKIEŁKO-WITKOWSKA A. Coordinated reprogramming of renal cancer transcriptome, metabolome and secretome associates with immune tumor infiltration. Cancer Cell International (2023) 23(1): 2 (15 p.) DOI: 10.1186/s12935-022-02845-y IF 5.3 (2023)
MIERZEJEWSKI B., MICHALSKA Z., JACKOWSKI D., STREMIŃSKA W., JAŃCZYK-ILACH K., KOBLOWSKA M., IWANICKA-NOWICKA R., GROMADKA A., CIEMERYCH M.A., BRZÓSKA E., The miR151 and miR5100 Transfected Bone Marrow Stromal Cells Increase Myoblast Fusion in IGFBP2 Dependent Manner. Stem Cell Reviews and Reports (2022) 18(6): 2164-2178 DOI: 10.1007/s12015-022-10350-y IF 4.8 (2022)
KOBRZYCKA A.T., STANKIEWICZ A.M., GOŚCIK J., GORA M., BURZYNSKA B., IWANICKA-NOWICKA R., PIERZCHAŁA-KOZIEC K., WIECZOREK M., Hypothalamic Neurochemical Changes in Long-Term Recovered Bilateral Subdiaphragmatic Vagotomized Rats. Frontiers in Behavioral Neuroscience (2022) 16: 869526 (8 p.) DOI: 10.3389/fnbeh.2022.869526 IF 3.0 (2022)
WILAMOWSKA A., KOBLOWSKA M., MATLAKOWSKA R., Postdiagenetic Changes in Kerogen Properties and Type by Bacterial Oxidation and Dehydrogenation. Molecules (2022) 27(8): 2408 (17 p.) DOI: 10.3390/molecules27082408 IF 4.6 (2022)
DASZCZYŃSKA A., KRUCOŃ T., STASIUK R., KOBLOWSKA M., MATLAKOWSKA R., Lanthanide-Dependent Methanol Metabolism of a Proteobacteria-Dominated Community in a Light Lanthanide-Rich Deep Environment. International Journal of Molecular Sciences (2022) 23(7): 3947 (15 p.) DOI: 10.3390/ijms23073947 IF 5.6 (2022)
KONWERSKI M., GROMADKA A., ARENDARCZYK A., KOBLOWSKA M., IWANICKA-NOWICKA R., WILIMSKI R., CZUB P., FILIPIAK K.J., HENDZEL P., ZIELENKIEWICZ P., OPOLSKI G., GĄSECKA A., MAZUREK T., Atherosclerosis pathways are activated in pericoronary adipose tissue of patients with coronary artery disease. Journal of Inflammation Research (2021) 14: 5419-5431 DOI: 10.2147/JIR.S326769 IF 4.631 (2021)
JAROŃCZYK K., SOSNOWSKA K., ZABOROWSKI A., PUPEL P., BUCHOLC M., MAŁECKA E., SIWIRYKOW N., STACHULA P., IWANICKA-NOWICKA R., KOBLOWSKA M., JERZMANOWSKI A., ARCHACKI R., Bromodomain-containing subunits BRD1, BRD2, and BRD13 are required for proper functioning of SWI/SNF complexes in Arabidopsis. Plant Communications (2021) 2(4): 100174 (15 p.) DOI: 10.1016/j.xplc.2021.100174 IF 8.625 (2021)
SHAHMORADI GHAHE S., KOSICKI K., WOJEWÓDZKA M., MAJCHRZAK B.A., FOGTMAN A., IWANICKA-NOWICKA R., CIUBA A., KOBLOWSKA M., KRUSZEWSKI M., TUDEK B., SPEINA E., Increased DNA repair capacity augments resistance of glioblastoma cells to photodynamic therapy. DNA Repair (2021) 104: 103136 DOI: 10.1016/j.dnarep.2021.103136 IF 4.354 (2021)
HETMAŃCZYK-SAWICKA K., IWANICKA-NOWICKA R., FOGTMAN A., CIEŚLA J., WŁODARSKI P., ŻYŻYŃSKA-GRANICA B., FILOCAMO M., DARDIS A., PERUZZO P., BEDNARSKA-MAKARUK M., KOBLOWSKA M., ŁUGOWSKA A., Changes in global gene expression indicate disordered autophagy, apoptosis and inflammatory processes and downregulation of cytoskeletal signalling and neuronal development in patients with Niemann-Pick C disease. Neurogenetics (2020) 21(2): 105-119 DOI: 10.1007/s10048-019-00600-6 IF 2.660 (2020)
KASPRZYCKA P., ARCHACKA K., KOWALSKI K., MIERZEJEWSKI B., ZIMOWSKA M., GRABOWSKA I., PIOTROWSKI M., RAFAŁKO M., RYŻKO A., IRHASHAVA A., SENDEROWSKI K., GOŁĄBEK M., STREMIŃSKA W., JAŃCZYK-ILACH K., KOBLOWSKA M., IWANICKA-NOWICKA R., FOGTMAN A., JANOWSKI M., WALCZAK P., CIEMERYCH M.A., BRZÓSKA E., The factors present in regenerating muscles impact bone marrow-derived mesenchymal stromal/stem cell fusion with myoblasts. Stem Cell Research & Therapy (2019) 10: 343 (17 p.) DOI: 10.1186/s13287-019-1444-1 IF 5.116 (2019)
BOGUSŁAWSKA J., POPŁAWSKI P., ALSEEKH S., KOBLOWSKA M., IWANICKA-NOWICKA R., RYBICKA B., KĘDZIERSKA H., GŁUCHOWSKA K., HANUSEK K., TAŃSKI Z., FERNIE A.R., PIEKIEŁKO-WITKOWSKA A. MicroRNA-mediated metabolic reprograming in renal cancer. Cancers (2019) 11(12): 1825 (21 p.) DOI: 10.3390/cancers11121825 IF 6.126 (2019)
ZARYCHTA-WIŚNIEWSKA W., BURDZIŃSKA A., ZIELNIOK K., KOBLOWSKA M., GALA K., PĘDZISZ P., IWANICKA-NOWICKA R., FOGTMAN A., AKSAMIT A., KULESZA A., ZOŁOCIŃSKA A., PĄCZEK L., The influence of cell source and donor age on the tenogenic potential and chemokine secretion of human mesenchymal stromal cells. Stem Cells International (2019) 2019: 1613701 (14 p.) DOI: 10.1155/2019/1613701 IF 3.869 (2019)
ŁUGOWSKA A., HETMAŃCZYK-SAWICKA K., IWANICKA-NOWICKA R., FOGTMAN A., CIEŚLA J., PURZYCKA-OLEWIECKA J.K., SITARSKA D., PŁOSKI R., FILOCAMO M., LUALDI S., BEDNARSKA-MAKARUK M., KOBLOWSKA M., Gene expression profile in patients with Gaucher disease indicates activation of inflammatory processes. Scientific Reports (2019) 9(1): 6060 (14 p.) DOI: 10.1038/s41598-019-42584-1 IF 3.998 (2019)
WŁODARCZYK A., LIRSKI M., FOGTMAN A., KOBLOWSKA M., BIDZIŃSKI G., MATLAKOWSKA R., The oxidative metabolism of fossil hydrocarbons and sulfide minerals by the lithobiontic microbial community inhabiting deep subterrestrial Kupferschiefer black shale. Frontiers in Microbiology (2018) 9: 972 (14 p.) DOI: 10.3389/fmicb.2018.00972 IF 4.259 (2018)
WIESYK A., IWANICKA-NOWICKA R., FOGTMAN A., ZAGORSKI-OSTOJA W., GORA-SOCHACKA A., Time-course microarray analysis reveals differences between transcriptional changes in tomato leaves triggered by mild and severe variants of potato spindle tuber viroid. Viruses (2018) 10(5): 257 (23 p.) DOI: 10.3390/v10050257 IF 3.811 (2018)
KOWALSKI K., KOLODZIEJCZYK A.S., SIKORSKA M., PŁACZKIEWICZ J., CICHOSZ P., KOWALEWSKA M., STREMIŃSKA W., JAŃCZYK-ILACH K., KOBLOWSKA M., FOGTMAN A., IWANICKA-NOWICKA R., CIEMERYCH M.A., BRZÓSKA E., Stem cells migration during skeletal muscle regeneration - the role of Sdf-1/Cxcr4 and Sdf-1/Cxcr7 axis. Cell Adhesion and Migration (2017) 11(4): 384-398 DOI: 10.1080/19336918.2016.1227911 IF 3.566 (2017)

Team