{"EMPIAR-12104":{"imagesets":[{"segmentations":[],"name":"Raw unaligned multi-frame micrographs for each tilt in 4 tilt-series on native S. cerevisiae cryo-FIB lamellae","directory":"data/Control/frames","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":203,"frames_per_image":10,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":3.425,"pixel_height":null,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Raw unaligned multi-frame micrographs were aligned, sorted and combined into tilt series stacks using Warp (st files in metadata folder) and tomograms reconstructed using AreTomo. Naming for tomograms of control cells: TS_006, TS_007, TS_008, TS_017. Original metadata files (mdocs_ori) and the count ref file (dm4 file) are provided in the frames folder.","image_width":"5760","image_height":"4092"},{"segmentations":[{"file":"data/Control/labels","description":"3D annotation volumes for ribosomes localised in 4x binned reconstructed tomograms (13.7 A voxel size) are provided in the labels folder.","original_files":null,"original_format":"MRC","entry":null}],"name":"Reconstructed cryo-electron tomograms acquired on native S. cerevisiae cryo-FIB lamellae","directory":"data/Control/tomograms","category":"reconstructed volumes","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":4,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":13.7,"pixel_height":13.7,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Tomograms (4-times binned reconstructions, original unbinned pixel size 3.425Å) from aligned frame stacks (st files in metadata folder, tif files in frames folder), mdoc and xf alignment files (in metadata folder). Naming for tomograms of control cells: TS_006, TS_007, TS_008, TS_017. For each of the 4 tomograms, cleaned particle lists are provided in the labels folder. Ribosome particle coordinates (star files) are provided in the corresponding particle_lists folder.","image_width":"1022","image_height":"1440"},{"segmentations":[],"name":"Tilt series stacks and metadata of cryo-electron tomograms acquired on native S. cerevisae cryo-FIB lamellae","directory":"data/Control/metadata","category":"tilt series","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":4,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":3.425,"pixel_height":3.425,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Tilt series stacks (st files from Warp) from aligned frame stacks (in frames folder), tilt series alignment files (xf files) and acquisition metadata files modified to exclude bad tilts (in mdocs_modified) required to reconstruct tomograms (in tomograms folder). Naming for tomograms of control cells: TS_006, TS_007, TS_008, TS_017.","image_width":null,"image_height":null},{"segmentations":[],"name":"Raw unaligned multi-frame micrographs for each tilt in 10 tilt-series acquired on S. cerevisiae cryo-FIB lamellae under acute glucose starvation","directory":"data/Acute_glucose_starvation/frames","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":565,"frames_per_image":10,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":3.425,"pixel_height":3.425,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Raw unaligned multi-frame micrographs were aligned, sorted and combined into tilt series stacks using Warp (st files in metadata folder) and tomograms reconstructed using AreTomo. Naming for tomograms of cells under glucose starvation: TS_001, TS_002, TS_003, TS_004, TS_007, TS_008, TS_010, TS_014, TS_017, TS_018. Original metadata files (mdocs_ori) provided in the frames folder.","image_width":"5760","image_height":"4092"},{"segmentations":[{"file":"data/Acute_glucose_starvation/labels","description":"3D annotation volumes for ribosomes localised in 4x binned reconstructed tomograms (13.7 A voxel size) are provided in the labels folder.","original_files":null,"original_format":"MRC","entry":null}],"name":"Reconstructed cryo-electron tomograms acquired on S. cerevisiae cryo-FIB lamellae under acute glucose starvation","directory":"data/Acute_glucose_starvation/tomograms","category":"reconstructed volumes","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":10,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":13.7,"pixel_height":13.7,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Tomograms (4-times binned reconstructions, original unbinned pixel size 3.425Å) from aligned frame stacks (st files in metadata folder, tif files in frames folder), mdoc and xf alignment files (in metadata folder). Naming for tomograms of cells under glucose starvation: TS_001, TS_002, TS_003, TS_004, TS_007, TS_008, TS_010, TS_014, TS_017, TS_018. For each of the 10 tomograms, cleaned particle lists are provided in the labels folder. Ribosome particle coordinates (starfiles) are provided in the corresponding particle_lists folder.","image_width":"1022","image_height":"1440"},{"segmentations":[],"name":"Tilt series stacks and metadata of cryo-electron tomograms acquired on S. cerevisae cryo-FIB lamellae under acute glucose starvation","directory":"data/Acute_glucose_starvation/metadata","category":"tilt series","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":10,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":3.425,"pixel_height":3.425,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Tilt series stacks (st files from Warp) from aligned frame stacks (in frames folder), tilt series alignment files (xf files) and acquisition metadata files modified to exclude bad tilts (in mdocs_modified) required to reconstruct tomograms (in tomograms folder). Naming for tomograms of cells under glucose starvation: TS_001, TS_002, TS_003, TS_004, TS_007, TS_008, TS_010, TS_014, TS_017, TS_018.","image_width":"5760","image_height":"4092"}],"workflow_file":null,"grant_references":[{"funding_body":"European Research Council (ERC)","code":"760067","country":"Germany"}],"version_history":[],"title":"Cryo-electron tomography data acquired on S. cerevisiae (BY4741) cryo-FIB lamellae","principal_investigator":[{"author_orcid":"0000-0001-6968-041X","middle_name":null,"organization":"European Molecular Biology Laboratory","street":"Meyerhofstrasse 1","town_or_city":"Heidelberg","state_or_province":null,"post_or_zip":"69117","telephone":"+49 (0)6221 387 8451","fax":null,"first_name":"Julia","last_name":"Mahamid","email":"julia.mahamid [at] embl.de","country":"Germany","entry":"EMPIAR-12104"}],"status":"REL","deposition_date":"2024-05-25","release_date":"2025-02-04","obsolete_date":null,"update_date":"2025-02-04","corresponding_author":{"author":{"author_orcid":"0000-0003-0300-3867","middle_name":null,"organization":"European Molecular Biology Laboratory","street":"Meyerhofstrasse 1","town_or_city":"Heidelberg","state_or_province":null,"post_or_zip":"69117","first_name":"Marie-Christin","last_name":"Spindler","country":"Germany"}},"authors":[{"author":{"name":"Spindler MC","author_orcid":"0000-0003-0300-3867"}},{"author":{"name":"Mahamid J","author_orcid":"0000-0001-6968-041X"}}],"cross_references":["EMD-50409","EMD-50415"],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Xie Y","author_orcid":null},{"name":"Shu T","author_orcid":"0000-0001-6036-0057"},{"name":"Liu T","author_orcid":null},{"name":"Spindler MC","author_orcid":null},{"name":"Mahamid J","author_orcid":null},{"name":"Hocky GM","author_orcid":"0000-0002-5637-0698"},{"name":"Gresham D","author_orcid":null},{"name":"Holt LJ","author_orcid":"0000-0002-4002-0861"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Polysome collapse and RNA condensation fluidize the cytoplasm","volume":"84","country":"","first_page":"2698","last_page":"2716.e9","year":"2024","language":"English","doi":"10.1016/j.molcel.2024.06.024","pubmedid":"39059370","details":"Deposition of 14 tomograms (4 for control cells in glucose rich media, and 10 for the acute glucose starvation condition) used to determine polysome assembly states.","book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"Molecular cell","journal_abbreviation":"Mol Cell","issue":"14","preprint":false}],"dataset_size":"165.4 GB","experiment_type":"EMDB","scale":"cell","entry_doi":"10.6019/EMPIAR-12104"}}