REL 2022-04-01 2024-01-16 2024-01-16 0000-0002-4159-6934 Eija Jokitalo Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki PL56 (Viikinkaari 9) Helsinki Uusimaa Finland 00014 0000-0002-4159-6934 Eija Jokitalo Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki PL56 (Viikinkaari 9) Helsinki Uusimaa Finland 00014 Belevich I Jokitalo E 8.7 10.6019/EMPIAR-10994 SBF-SEM cell Kumar D Golchoubian B Belevich I Jokitalo E Schlaitz AL Molecular biology of the cell Mol Biol Cell 12 30 1377 1389 2019 English 10.1091/mbc.e18-11-0698 30995177

SBF-SEM datasets of control and REEP3/4 KD HeLa cells in metaphase

HeLa Control metaphase cell, raw data /data/160621_HeLa_Control/01_original_images micrographs - single frame DM4 DM4 578 1 UNSIGNED 16 BIT INTEGER 1280 151.884 1280 151.884

Z voxel size is 30 nm

data/160621_HeLa_Control/03_models Two models, one (CellOutlineModel_TIF and Labels_cell_outlines.mask) for outlines of the metaphase cell, and the other (OrganelleModel_TIF and Labels_160621_HeLa_OrganelleModel.model) includes segmentation of mitochondria, chromosomes, centrioles, and ER from a quadrant of the cell and insides of the spindle area. Z voxel size is 30 nm Labels_cell_outlines.mask and Labels_160621_HeLa_OrganelleModel.model are a mask and a model files for Microscopy Image Browser Description of materials is available in readme.txt file and shown below: Model of one quadrant of a metaphase HeLa cell Labels_160621_HeLa_OrganelleModel.model -> model file of segmented organelles in Microscopy Image Browser format OrganelleModel_TIF -> the same model in TIF format Indices of materials: 0 -> Exterior 1 -> Mitochondria 2 -> ER 3 -> ER at the close proximity to chromosomes (at 320 nm distance) 4 -> Chromosomes 5 -> Centrioles 6 -> Peripheral ER Labels_cell_outlines.mask -> model mask file of segmented cell outline CellOutlineModel_TIF -> the same model in TIF format data/160621_HeLa_Control/03_models TIFF data/161107_HeLa_REEP3-4_KD_LBR/03_models A model (Model_TIF and Labels_161107_HeLa_REEP3-4_KD_LBR.model) includes segmentation of mitochondria, chromosomes, lipid droplets, and ER from a quadrant of the cell and insides of the spindle area. Z voxel size is 30 nm Labels_161107_HeLa_REEP3-4_KD_LBR.model is a model file for Microscopy Image Browser Description of materials is available in readme.txt file and shown below: Model of one quadrant of a metaphase HeLa REEP 3/4 KD LBR cell Labels_161107_HeLa_REEP3-4_KD_LBR.model -> model file of segmented organelles in Microscopy Image Browser format Model_TIF -> the same model in TIF format Indices of materials: 0 -> Exterior 1 -> Mitochondria 2 -> Lipid Droplets 3 -> ER 4 -> Chromosomes data/161107_HeLa_REEP3-4_KD_LBR/03_models TIFF HeLa Control metaphase cell, processed data /data/160621_HeLa_Control/02_processed_dataset micrographs - single frame TIFF TIFF 578 1 UNSIGNED BYTE 1453 151.884 1477 151.884

Z voxel size is 30 nm

HeLa REEP3/4 KD metaphase cell, raw datasets /data/161107_HeLa_REEP3-4_KD_LBR/01_original_images micrographs - single frame DM4 DM4 474 1 UNSIGNED 16 BIT INTEGER 1400 148.183 1400 148.183

Z voxel size is 30 nm

HeLa REEP3/4 KD metaphase cell, processed datasets /data/161107_HeLa_REEP3-4_KD_LBR/02_processed_dataset micrographs - single frame TIFF TIFF 471 1 UNSIGNED BYTE 1600 148.183 1586 148.183

Z voxel size is 30 nm