Data-deposition protocols for correlative soft X-ray tomography and super-resolution structured illumination microscopy applications

Andrii Iudin; Ugis Sarkans; Mohamed A Koronfel; Tom Fish; Ian Dobbie; Maria Harkiolaki; Ardan Patwardhan; Gerard J Kleywegt

doi:10.1016/j.xpro.2020.100253

Data-deposition protocols for correlative soft X-ray tomography and super-resolution structured illumination microscopy applications

STAR Protoc. 2021 Jan 13;2(1):100253. doi: 10.1016/j.xpro.2020.100253. eCollection 2021 Mar 19.

Authors

Andrii Iudin¹, Ugis Sarkans¹, Mohamed A Koronfel², Tom Fish², Ian Dobbie³, Maria Harkiolaki², Ardan Patwardhan¹, Gerard J Kleywegt¹

Affiliations

¹ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
² Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DW, UK.
³ Micron, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.

Abstract

This protocol illustrates the steps necessary to deposit correlated 3D cryo-imaging data from cryo-structured illumination microscopy and cryo-soft X-ray tomography with the BioStudies and EMPIAR deposition databases of the European Bioinformatics Institute. There is currently a real need for a robust method of data deposition to ensure unhindered access to and independent validation of correlative light and X-ray microscopy data to allow use in further comparative studies, educational activities, and data mining. For complete details on the use and execution of this protocol, please refer to Kounatidis et al. (2020).

Keywords: Bioinformatics; Cell Biology; Microscopy; Structural Biology.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Databases, Factual*
Imaging, Three-Dimensional*
Tomography, X-Ray*

Abstract

Publication types

MeSH terms

Grants and funding