DOI: 10.5061/dryad.9s4mw6mp4
title: Data from: Atlas of Plasmodium falciparum intraerythrocytic development using expansion microscopy

description: Apicomplexan parasites exhibit tremendous diversity in much of their
 fundamental cell biology, but study of these organisms using light
 microscopy is often hindered by their small size. Ultrastructural
 expansion microscopy (U-ExM) is a microscopy preparation method that
 physically expands the sample ∼4.5x. Here, we apply U-ExM to the human
 malaria parasite Plasmodium falciparum during the asexual blood stage of
 its lifecycle to understand how this parasite is organized in
 three-dimensions. Using a combination of dye-conjugated reagents and
 immunostaining, we have catalogued 13 different P. falciparum structures
 or organelles across the intraerythrocytic development of this parasite
 and made multiple observations about fundamental parasite cell biology. We
 describe that the microtubule organizing center (MTOC) and its associated
 proteins anchor the nucleus to the parasite plasma membrane during
 mitosis. Furthermore, the rhoptries, Golgi, basal complex, and inner
 membrane complex, which form around this anchoring site while nuclei are
 still dividing, are concurrently segregated and maintain an association to
 the MTOC until the start of segmentation. We also show that the
 mitochondrion and apicoplast undergo sequential fission events while
 maintaining an MTOC association during cytokinesis. Collectively, this
 study represents the most detailed ultrastructural analysis of P.
 falciparum during its intraerythrocytic development to date, and sheds
 light on multiple poorly understood aspects of its organelle biogenesis
 and fundamental cell biology.
description: This dataset comprises 647 images of <em>Plasmodium
 falciparum</em> parasites acquired using Airyscan microscopy on
 either a Zeiss LSM 800, or Zeiss LSM 900 microscope using a 63x Plan
 Apochromat 1.4NA objective lens. All images in this dataset have been
 Airyscan processed in 3D using the "standard" filter setting.
 Raw, non-airyscanned, images are available upon request, but have not been
 included in this dataset as they cannot be used in many of the most
 commonly used microscopy image analysis programs. Channels for fluorescent
 markers have been changed to reflect the colouring system used in the
 corresponding manuscript. While image colour combinations vary for some
 images, they broadly follow the trend: Cyan = SYTOX Deep Red (DNA stain),
 Magenta = antibody stain of interest (typically Alexa Fluor 488), Inverse
 greyscale = NHS ester Alexa Fluor 405 (protein stain), White =
 BODIPYTexasRed Ceramide (lipid stain), Yellow = second antibody stain of
 interest (typically Alexa Fluor 555), or MitoTracker CMTMRos
 (mitochondrial stain).
description: # Atlas of *Plasmodium falciparum* intraerythrocytic development using
 expansion microscopy
 [https://doi.org/10.5061/dryad.9s4mw6mp4](https://doi.org/10.5061/dryad.9s4mw6mp4) This dataset contains all images that support the study entitled "Atlas of *Plasmodium falciparum* intraerythrocytic development using expansion microscopy" published in eLife (https://doi.org/10.7554/eLife.88088.1) ## Description of the data and file structure Each of the files included in this dataset is a .czi file corresponding to an Airyscan-processed image of a single *Plasmodium falciparum* parasite. Files are named using the following convention: Parasite line_ Fluorescence Channel 1_Fluorescence Channel 2_Fluorescence Channel 3_Fluorescence Channel 4_Airyscan Processed (Image number).czi Fluorescence channels are ordered from shortest wavelength (in nm) to longest. Channels corresponding to antibody stains have the name of the target protein followed by the wavelength of the conjugated fluorophore. Image number does not follow any particular order, and only represents the number of images for that particular parasite line and fluorophore combination. For example: 3D7_NHS405_Aldolase488_BODIPYTRc_SytoxRed_Airyscan Processed (1).czi A small number of images in the dataset were of parasites fixed using a combination of paraformaldehyde (PFA) and glutaraldehyde (glut). These use the naming convention: Parasite line (PFA-Glut)_Fluorescence Channel 1_Fluorescence Channel 2_Fluorescence Channel 3_Fluorescence Channel 4_Airyscann Processed (Image number).czi **Images of the following parasite lines are represented in this database:** *Plasmodium falciparum* 3D7 *Plasmodium falciparum* 3D7_ACP-TS-GFP (referred to as ACP-TS-GFP in the dataset) *Plasmodium falciparum* 3D7_ATP_Synthase_F0 Subunit_d(Pf3D7_0311800)_smHA (referred to as ATPd in the dataset) *Plasmodium falciparum* 3D7_CINCH(Pf3D7_0407800)_smV5 (referred to as CINCHsmV5 in the dataset) *Plasmodium falciparum* 3D7_Kelch13WT_GFP (referred to as K13-GFP in the dataset) **Commonly used colours for fluorescence channels represented in this dataset:** NHS Ester Alexa Fluor 405 (Protein stain) = Inverse Greyscale BODIPY Tr Ceramide (Lipid stain) = White Protein of interest A = Magenta SYTOX Deep Red (DNA stain) = Cyan Protein of interest B or MitoTracker CMTMRos = Yellow **The following abbreviations are used in the naming of images of the dataset:** NHS = N-hydroxysuccinimdyl ester Alexa Fluor 405 BODIPY TRc = BODIPY Texas Red Ceramide Sytox Red = SYTOX Deep Red EBA175 = Erythrocyte Binding Antigen 175 AMA1 = Apical Membrane Antigen 1 RAMA = Rhoptry Apical Membrane Antigen RAP1 = Rhoptry Associated Protein 1 IMC1g = Inner-membrane Complex Protein 1g MSP1 = Merozoite Surface Protein 1 GAP45 = Glideosome Associated Protein 45 RON4 = Rhoptry Neck Protein 4 GFP = Green Fluorescence Protein ACP-TS = Acyl carrier protein apicoplast targeting signal ATPd = ATP Synthase Subunit F0 d sm = spaghetti monster tag K13 = Kelch13 PFA = Paraformaldehyde Glut = Glutaraldehyde ## Sharing/Access information All data in this dataset was generated for, and underlies the conclusion of the following study: * [https://doi.org/10.7554/eLife.88088.1](https://doi.org/10.7554/eLife.88088.1)