Single Cell (sc) Analysis Unit is a new core facility initiative with the mission to provide analysis services and technical support to researchers wanting to conduct single cell Next Generation Sequencing (scNGS) studies. We offer our expertise and computational space to support our clients’ research by providing analysis services for a wide range of single cell assays including scRNA-seq (single cell profiling of the transcriptome), scATAC-seq (single cell profiling of the epigenome), and spatial transcriptomics.
Our team offers end-to-end single-cell analysis solutions, using state-of-the art bioinformatics methodologies and in-house analysis pipelines, in order to offer structured, high quality and reproducible analysis deliverables. We also want to guide our community to have easy access to primary analysis solutions, and we aim to develop novel algorithms that will interpret the high-dimensional single-cell information in order to answer complex biological questions.
The Unit has recently developed SCALA (Single Cell AnaLysis for All), an R/Shiny web application and stand-alone toolkit, that handles the analysis of scRNA-seq and scATAC-seq datasets. It offers various modes of analysis including quality control, normalization, dimensionality reduction, differential expression/accessibility analysis, cell clustering, functional enrichment analysis, trajectory inference, ligand – receptor analysis, gene regulatory network inference, and visualization. For more information and to try out the web version of the tool, please visit - http://scala.fleming.gr/app/scala , or visit - https://github.com/PavlopoulosLab/SCALA to install it locally.
Unit development is supported by the Hellenic Foundation for Research & Innovation (HFRI) ELIDEK; 1st Call for H.F.R.I. Research Projects to Support Faculty Members & Researchers and Procure High-Value Research Equipment (Grant ID: 3780) to G. Kollias.
Unit Members
Konstantinos Apostolou-Karampelis / Postdoctoral Fellow
Christos Tzaferis / Ph.D. student
Publications
Armaka M, Konstantopoulos D, Tzaferis C, Lavigne MD, Sakkou M, Liakos A, Sfikakis PP, Dimopoulos MA, Fousteri M & Kollias G. 2022, "Single-cell multimodal analysis identifies common regulatory programs in synovial fibroblasts of rheumatoid arthritis patients and modeled TNF-driven arthritis", Genome Med. , 14(1) :78. [PubMed].
Tzaferis C, Karatzas E, Baltoumas FA, Pavlopoulos GA, Kollias G, Konstantopoulos D. 2022, "SCALA: A web application for multimodal analysis of single cell next generation sequencing data", bioRxiv, [doi].
Detsika MG, Sakkou M, Triantafyllidou V, Konstantopoulos D, Grigoriou E, Psarra K, Jahaj E, Dimopoulou I, Orfanos SE, Tsirogianni A and Kollias G, 2022. "Upregulation of CD55 complement regulator in distinct PBMC subpopulations of COVID-19 patients is associated with suppression of interferon responses", bioRxiv, [doi].
Phone Number
+30 210 9656310 (ext. 203)
Email
Address
BSRC "Alexander Fleming"
34 Fleming Street, 16672
Vari, Greece