DOI: 10.5281/zenodo.17464498
title: A toolkit for testing membrane-localising tags across species

description: Supplementary data for Karapidaki et al., 'A toolkit for testing membrane-localising tags across species'

 

The supplementary data include:

Membrane tags toolkit (.zip file): Annotated DNA sequences of the constructs comprising our toolkit and of the plasmid vector in which they are cloned, in genbank (.gb) format.

Caenorhabditis (.zip file): Confocal imaging data of Caenorhabditis embryos deriving from gonads injected with each of the reporters, used to prepare Figure S5, in .tif format. Each folder contains confocal image stacks with 3 channels – for brightfield, green autofluorescence, and mScarlet3 – and the associated metadata. The data were generated by Clayton Pavlich and Daniel Dickinson.

Clytia (.zip file): Confocal imaging data of Clytia blastula-stage embryos and primary polyps injected with each of the reporters, in .tif format. The four folders contain image stacks from blastula embryos (figures 5 and S9) and polyps (figures S10), the images for figure S15, and those used to quantify fluorescence; the latter folder includes the quantifications in .xlsx format. The data were generated by Sarah Assaf, Tsuyoshi Momose and Evelyn Houliston.

Macrostomum (.zip file): Confocal imaging data of Macrostomum embryos injected with each of the reporters, used to prepare Figure S8, in .tif format. The two folders contain the image stacks used to generate the figure and to quantify the fluorescence; the latter includes the quantifications in .xlsx format. The image files have separate channels capturing H2B-mNeonGreen (nuclear marker used as injection control) and the mScarlet3 fluorescence. The data were generated by Mattia Stranges, Kirill Ustyantsev and Eugene Berezikov.

Nematostella (.zip file): Confocal imaging data of Nematostella embryos injected with each of the reporters, used to prepare Figure S13, in .tif format. Each folder contains data from two channels, capturing fluorescence from phalloidin staining and mScarlet3 from the same embryos (labelled ch00 and ch01). The data were generated by Grigory Genikhovich.

Paracentrotus (.zip file): Confocal imaging data of Paracentrotus embryos injected with each of the reporters, in .tif format. The files are organised in four folders, containing the images used to prepare figures 3, S2 and S14, and to quantify the fluorescence; the latter includes the quantifications in .xlsx format. The image files have separate channels for mScarlet3 fluorescence and brightfield imaging. The data were generated by Maria Lorenza Rusciano and Maria Ina Arnone.

Parhyale (.zip file): Confocal and light sheet imaging data of Parhyale embryos injected with each of the reporters, in .tif format. The files are organised in four folders, containing the images used to prepare figure S4 (confocal_microscopy), figure 4 (light_sheet_microscopy), figure 8, and video S1. The first folder includes the images that were quantified, and a file with the quantifications in .xlsx format. We also include annotated DNA sequences of constructs used to generate transgenic Parhyale (see figure 8), in genbank format. The data were generated by Irene Karapidaki, Marie Zilliox, Beryl Laplace-Builhé, Manon Koenig and Michalis Averof.

Pelagia (.zip file): Confocal imaging data of Pelagia gastrula-stage embryos and planula larvae injected with each of the reporters, used to prepare Figures S11 and S12, in .tif format. The data were generated by Clara Deleau and Lucas Leclère.

Phallusia (.zip file): Confocal image data for Phallusia embryos injected with each of the reporters, used to prepare figures 2 and S1, in .tif format; each folder contains the images used to prepare the figures and additional datasets used to quantify the localisation. A file with the quantifications, in .xlsx format, is also included. The data were generated by Hitoyoshi Yasuo.

Platynereis (.zip file): Light sheet image data of Platynereis embryos and larvae injected with each of the reporters, used to prepare Figures S6 and S7, in .tif format. We provide images that were reconstructed from multiple views. The data were generated by Mette Handberg-Thorsager, Beke Lohmann and Jan Huisken.

Salpingoeca (.zip file): Confocal image data of Salpingoeca cells expressing mStayGold-KRas and untransfected controls, used to prepare Figure 7, in .tif format, and the annotated DNA sequence of the reporter plasmid, in genbank format. The data were generated by Juliette Mathieu and Thibaut Brunet.

Tribolium (.zip file): Confocal imaging data of Tribolium embryos injected with each of the reporters, used to prepare Figure S3, in .tif format. Each folder contains low- and/or high-magnification views (20X and 40X). The data were generated by Ying Pang and Gregor Bucher.

Video S1 (.avi file): Dynamics of SP-CD8tm-mScarlet3 localisation in a Parhyale embryo injected with reporter #10 mRNA at the 1-cell stage. The embryo was imaged on a confocal microscope at 20-minute time intervals. The video shows a maximum projection of multiple confocal sections, starting approximately 24 hours after injection. Scale bar, 20 µm. Data generated by Manon Koenig, Béryl Laplace-Builhé and Irene Karapidaki.