Inferring spatially transient gene expression pattern from spatial transcriptomic studies

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract Spatial transcriptomic is a technology to provide deep transcriptomic profiling by preserving the spatial organization. Here, we present a framework for SPAtial Transcriptomic Analysis (SPATA, https://themilolab.github.io/SPATA ), to provide a comprehensive characterization of spatially resolved gene expression, regional adaptation of transcriptional programs and transient dynamics along spatial trajectories.

Authors 10

1. Jan Kueckelhaus

   University of Freiburg · University Medical Center Freiburg

   Affiliation as printed

   Department of Neurosurgery, Medical Center, University of Freiburg, Germany

   Faculty of Medicine, Freiburg University, Germany

   Microenvironment and Immunology Research Laboratory, Medical Center, University of Freiburg, Germany

2. Jasmin von Ehr

   University of Freiburg · University Medical Center Freiburg

   Affiliation as printed

   Department of Neurosurgery, Medical Center, University of Freiburg, Germany

   Faculty of Medicine, Freiburg University, Germany

   Microenvironment and Immunology Research Laboratory, Medical Center, University of Freiburg, Germany

3. Vidhya Madapusi Ravi

   University of Freiburg · University Medical Center Freiburg

   Affiliation as printed

   Department of Neurosurgery, Medical Center, University of Freiburg, Germany

   Faculty of Medicine, Freiburg University, Germany

   Microenvironment and Immunology Research Laboratory, Medical Center, University of Freiburg, Germany

4. Paulina Will

   University of Freiburg · University Medical Center Freiburg

   Affiliation as printed

   Department of Neurosurgery, Medical Center, University of Freiburg, Germany

   Faculty of Medicine, Freiburg University, Germany

   Microenvironment and Immunology Research Laboratory, Medical Center, University of Freiburg, Germany

5. Kevin Joseph

   University of Freiburg · University Medical Center Freiburg

   Affiliation as printed

   Department of Neurosurgery, Medical Center, University of Freiburg, Germany

   Faculty of Medicine, Freiburg University, Germany

   Microenvironment and Immunology Research Laboratory, Medical Center, University of Freiburg, Germany

6. Jürgen Beck

   University of Freiburg · University Medical Center Freiburg

   Affiliation as printed

   Department of Neurosurgery, Medical Center, University of Freiburg, Germany

   Faculty of Medicine, Freiburg University, Germany

7. Ulrich Hofmann

   University of Freiburg · University Medical Center Freiburg

   Affiliation as printed

   Faculty of Medicine, Freiburg University, Germany

   Neuroelectronic Systems, Medical Center, University of Freiburg, Germany

8. Daniel Delev Aachen Department of Neurosurgery Neurosurgical Artificial Intelligence Laboratory Aachen (NAILA)

   RWTH Aachen University

   Affiliation as printed

   Department of Neurosurgery, RWTH University of Aachen, Aachen, Germany

   Neurosurgical Artificial Intelligence Laboratory Aachen (NAILA), Department of Neurosurgery, RWTH University of Aachen, Aachen, Germany

9. Oliver Schnell

   University of Freiburg · University Medical Center Freiburg

   Affiliation as printed

   Department of Neurosurgery, Medical Center, University of Freiburg, Germany

   Faculty of Medicine, Freiburg University, Germany

   Translational NeuroOncology Research Group, Medical Center, University of Freiburg, Germany

10. Dieter Henrik Heiland corresponding

    University of Freiburg · University Medical Center Freiburg

    Affiliation as printed

    Department of Neurosurgery, Medical Center, University of Freiburg, Germany

    Faculty of Medicine, Freiburg University, Germany

    Microenvironment and Immunology Research Laboratory, Medical Center, University of Freiburg, Germany