Munich Cluster for Systems Neurology

Breadcrumb Navigation


Transcriptome Hub

Single-cell Transcriptome Hub

1.0 Objective
1.1 Organisation
1.2 Technical portfolio
1.3 Project request procedure
1.4 Fees
1.5 Publications


1.0 Objective

The Single-cell Transcriptome Hub has been established since 2019 to focus on single cells analyses, which are extraordinarily valuable tools in biomedicine. These technologies allow us to identify transcriptional profiles of distinct cells that fulfill certain characteristics such as location in tissue, morphology, expression of markers for activation, homing, and many others.

The scTranscriptome Hub offers the full range of analytical equipment and technologies to analyze single cell transcriptomes from any cell and organism of interest. Under certain conditions even FFPE fixed samples and archival human tissue may be analyzed. Our technologies are not restricted to any particular cell type, we may analyze any cell type involved in inflammatory, degenerative, or gliovascular conditions of the nervous system.

The scTranscriptome Hub aims to provide single cell genomic experimental support to primarily SyNergy projects but also external projects depending on their general technical or scientific impact and benefit for future cluster-internal projects.

Please contact the Single-cell Transcriptome Hub group leaders for project requests or further questions ( or

1.1 Organisation

The Single-cell Transcriptome Hub in located at the BioMedical Building (BMC) in Martinsried and the Institute for Stroke and Dementia Research, LMU Klinikum

Name Function Location Mail phone
Eduardo Beltrán Hub group leader BMC,
N.B. 03.024 089-2180-71671
Mikael Simons Hub group leader DZNE


Jürgen Bernhagen
FACSsort leader ISD


Ozgun Gokce FACSsort co-leader ISD


Markus Utzt Technical Assistant BMC,
N.B. 03.024



1.2 Technical portfolio

Laser Capture Microdissection at BMC. Zeiss Microbeam Z

LCM allows us to isolate single cells, supracellular aggregates, or subcellular organells from frozen or FFPE tissue. Tissue may or may not be stained by immunohistochemistry. Under certain conditions, isolation of living cells is possible.



FACSort at BMC (contact: Core Facility Flow Cytometry at Biomedical Center Munich) or ISD (contact:

We have access to BD FACSAria Fusion and Sony SH800 cell sorters that allows us to isolate single cells after 8 to 6 color staining and sorting single cell into 96 or 384 well plates.



10x Genomics at BMC (contact: Eduardo Beltrán).

10x Genomics solutions allow us to profile simultaneously the whole transcriptome of up to ten thousands of single cells (scRNA-seq) or single nuclei (snRNA-seq) for sample. The Single Cell Immune Profiling provide a multiomic solution to profile full length paired B-cell or T-cell receptors as well as gene expression within a single human or mouse sample. In addition, for all 10x kits is possible to use Cell Hashing and measure Cell Surface Protein expression and CRISPR perturbations. We use an Agilent Bioanalyzer and Qubit for quality control.



smartseq2 at ISD (contact: Ozgun Gokce).

This approach allows us to prepare full length single cell cDNA libraries from 96 or 384 well plates for follow-up NGS analysis.




1.3 Project request procedure





1.4 Fees

 Budgeted on a per-project-basis (typically only consumables costs).


1.5 Publications

Beltrán E, Paunovic M, Gebert D, Cesur E, Jeitler M, Höftberger R, Malotka J, Mader S, Kawakami N, Meinl E, Bradl M, Dornmair K, Lassmann H. Archeological neuroimmunology: Resurrection of a pathogenic immune response from a historical case sheds light on human autoimmune encephalomyelitis and multiple sclerosis. Acta Neuropathologica doi: 10.1007/s00401-020-02239-2. Online ahead of print

Stanley G.*, Gokce O.*, Malenka R.C., Südhof T.C., and Quake S.R., (2020) Discrete and Continuous Cell Identities of the Adult Murine Striatum. Neuron 105 (4), 688-699. e8

Cantuti-Castelvetri, L., Ojha, R.,..., Gokce O., et al.,Simons M. (2020) Neuropilin-1 facilitates SARS-CoV-2 cell entry and provides a possible pathway into the central nervous system. Science eabd298

Bracher A, Alcalá C, Ferrer J, Melzer N, Hohlfeld R, Casanova B, Beltrán E, Dornmair K. An expanded parenchymal CD8+ T cell clone in GABAA receptor encephalitis. Ann Clin Transl Neurol. 2020 Jan 14. doi: 10.1002/acn3.50974

Beltrán E, Gerdes LA, Hansen J, Flierl-Hecht A, Krebs S, Blum H, Ertl-Wagner B, Barkhof F, Kümpfel T, Hohlfeld R, Dornmair K. Early adaptive immune activation detected in monozygotic twins with prodromal multiple sclerosis. J Clin Invest. 2019 Sep 30. pii: 128475. doi: 10.1172/JCI128475

Beltrán E, Nguyen XH, Quériault C, Barateau L, Dauvilliers Y, Dornmair K, Liblau RS. Shared T cell receptor chains in blood memory CD4+ T cells of narcolepsy type 1 patients. J Autoimmun. 2019 Apr 2. pii: S0896-8411(19)30048-4. doi: 10.1016/j.jaut.2019.03.010

Konjevic Sabolek M, Held K, Beltrán E, Niedl AG, Meinl E, Hohlfeld R, Lassmann H, Dornmair K Communication of CD8+ T cells with mononuclear phagocytes in multiple sclerosis. Ann Clin Transl Neurol. 2019 Jul;6(7):1151-1164. doi: 10.1002/acn3.783

Gokce O.*, Stenley G.*, Treutlein B*., Neff N.F., Camp G.J., Malenka R.C., Rothwell P.E., Fuccillo M.V., Südhof T.C. and Quake S.R., (2016) Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNAseq. Cell Reports 16, 1–12

Fuccillo M.*, Foldy C.*, Gokce O.*, Rothwell P.E., Sun G.L., Robert C.M. and Südhof T.C., (2015) Single-Cell mRNA Profiling Reveals Cell-Type-Specific Expression of Neurexin Isoforms. Neuron 87, 326–340.

Treutlein B*., Gokce O.*, Quake S.R., and Südhof T.C., (2014) Cartography of Neurexin Diversity Mapped by Single-Molecule Long-Read mRNA Sequencing. (PNAS) 111 (13) E1291-E1299;