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Published April 1, 2020 | Version v2.0

Raw data for the manuscript under the title "Mitochondrial RNA granules are fluid condensates, positioned by membrane dynamics".

  • 1. LEB, EPFL
  • 2. University of Geneva

Description

This is the data-repository to contain all relevant raw-data used and referred to in the manuscript entitled:
"Mitochondrial RNA granules are fluid condensates, positioned by membrane dynamics"
[manuscript under revision, and thus not citable as published article]

The repository is structured analogous to the manuscript and holds the data for:

Figure 1: 1-colour STORM data, 2-colour STORM data
      What should be considered the raw-data for SMLM-studies is a matter of debate. While the localisation-software as well as the specified parameters used therein can greatly influence the final analysis, in principle all raw-images should be provided as raw-data. However, this would result in excessive data-volumes required for our study. We therefore decided to upload only raw-localisations here. Raw image-stacks can be provided upon reasonable request to the authors directly.
       For all 1C-STORM acquisitions, Alexa-647 was used and localisations were extracted from raw images using sCMOS adapted software [Huang F. et al., Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms Nat Methods 7, 654:658, doi:10.1038/nmeth.2488 (2013)] as previously described here: Douglass, K. M. et al. Super-resolution imaging of multiple cells by optimised flat-field epi-illumination. Nat Photonics 10, 705–708, doi:10.1038/nphoton.2016.200 (2016),  and here: Sieben, C. et al. Multicolor single-particle reconstruction of protein complexes. Nat Methods 15, 777–780, doi:10.1038/s41592-018-0140-x (2018). We used kernel-sizes = 3, 7, and 3 for all data & the threshold 40 for BrU-data and threshold = 100 for all other data-sets.
       In 2C-STORM, BrU-localisations were generated analogous to 1C, while FASTKD2 was labelled with dyLight 755 secondary antibodies. Here, the kernel-sizes were set to 3, 7, 3 and thresold = 27 for data acquired in 2018, whereas the more recent data was found to be less bright at the same microscope-settings and thus the localisation parameters for late 2019 & early 2020 data were set to 3, 5, 3 for kernel sizes and 10 as a threshold-value.

Figure 2: FRAP- and live-cell SIM-data

Figure 3 & 4: EM-, STED-, and SIM-data

Notes

We are currently updating the files for re-submission. Beware of changes in the file-structure and content.

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