{"EMPIAR-12534":{"imagesets":[{"segmentations":[],"name":"Raw unaligned frame and metadata for each tilt in tilt-series acquired on CHX-treated S. cerevisiae cryo-FIB lamellae","directory":"data/EMPIAR_upload/Frames","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":462,"frames_per_image":11,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":1.663,"pixel_height":1.663,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Raw unaligned frames were preprocessed in Warp to generate tilt series stacks. Corresponding count reference files (mrc file) are in the subfolders of the EMPIAR_upload/Frames folder. The number of frames per image varies from 38 to 42. Subfolder names with YTC041_1, YTC041_2, and YTC042_2 are datasets acquired on S. cerevisiae grown in YPG. Subfolder names with YTC043_1 and YTC043_2 are datasets acquired on S. cerevisiae grown in YPD.","image_width":"5760","image_height":"4092"},{"segmentations":[],"name":"Unaligned tilt series stack of cryo-electron tomography acquired on CHX-treated S. cerevisiae cryo-FIB lamellae","directory":"data/EMPIAR_upload/Tilt_series","category":"tilt series","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":38,"frames_per_image":11,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":1.663,"pixel_height":1.663,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"The tilt series stacks (.st file) and rawtlt files (in Tilt_series_rawtlt) were created from Warp with the input of tilt-corrected mdoc files. Raw mdoc files are listed in the EMPIAR_upload/PACE_mdoc folder. Tilt series stacks are then aligned in IMOD.","image_width":"5760","image_height":"4092"},{"segmentations":[{"file":"data/EMPIAR_upload/Voxel_segmentations","description":"Voxel segmentations of mitochondrial outer and inner membrane","original_files":"data/EMPIAR_upload/Reconstructed_tomograms","original_format":"MRC","entry":null},{"file":"data/EMPIAR_upload/Surfaces","description":"Polygon Surface meshes generated from voxel segmentations using 'Surface_Morphometrics' for all membranes from mitochondria","original_files":"data/EMPIAR_upload/Reconstructed_tomograms","original_format":"STL","entry":null}],"name":"Reconstructed tomograms of CHX-treated S. cerevisiae lamellae used for segmentation of mitochondria","directory":"data/EMPIAR_upload/Reconstructed_tomograms","category":"reconstructed volumes","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":38,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":9.98,"pixel_height":9.98,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Bin6 tomograms are reconstructed from Warp after IMOD alignment. The coordinates of 80S ribosome and co-translating ribosome are provided in the EMPIAR_upload/Particle_lists folder.","image_width":"682","image_height":"960"},{"segmentations":[],"name":"Raw unaligned frame and metadata for each tilt in tilt-series acquired on vehicle-treated S. cerevisiae cryo-FIB lamellae","directory":"data/EMPIAR_upload_nonCHX/Frames","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":492,"frames_per_image":12,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":2.638,"pixel_height":2.638,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Raw unaligned frames were preprocessed in Warp to generate tilt series stacks. Corresponding count reference files (mrc file) are in the subfolders of the EMPIAR_upload_nonCHX/Frames folder. The number of frames per image varies from 39 to 41. Subfolder name with YTC009_3 is the dataset acquired on S. cerevisiae grown in YPG, and subfolder name with YTC025_2 is the dataset acquired on S. cerevisiae grown in YPD.","image_width":"5760","image_height":"4092"},{"segmentations":[],"name":"Unaligned tilt series stack of cryo-electron tomography acquired on vehicle-treated S. cerevisiae cryo-FIB lamellae","directory":"data/EMPIAR_upload_nonCHX/Tilt_series","category":"tilt series","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":49,"frames_per_image":12,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":2.638,"pixel_height":2.638,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"The tilt series stacks (.st file) and rawtlt files (in EMPIAR_upload_nonCHX/Tilt_series_rawtlt) were created from Warp with the input of tilt-corrected mdoc files. Raw mdoc files are listed in the EMPIAR_upload_nonCHX/mdocs folder. Tilt series stacks are then aligned in IMOD.","image_width":"5760","image_height":"4092"},{"segmentations":[{"file":"data/EMPIAR_upload_nonCHX/Voxel_segmentations","description":"Voxel segmentations of mitochondrial outer and inner membrane","original_files":"data/EMPIAR_upload_nonCHX/Reconstructed_tomograms","original_format":"MRC","entry":null},{"file":"data/EMPIAR_upload_nonCHX/Surfaces","description":"Polygon Surface meshes generated from voxel segmentations using 'Surface_Morphometrics' for all membranes from mitochondria","original_files":"data/EMPIAR_upload_nonCHX/Reconstructed_tomograms","original_format":"STL","entry":null}],"name":"Reconstructed tomograms of vehicle-treated S. cerevisiae lamellae used for segmentation of mitochondria","directory":"data/EMPIAR_upload_nonCHX/Reconstructed_tomograms","category":"reconstructed volumes","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":49,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":15.83,"pixel_height":15.83,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Bin6 tomograms are reconstructed from Warp after IMOD alignment. The coordinates of 80S ribosome and co-translating ribosome are provided in the EMPIAR_upload_nonCHX/Particle_lists folder.","image_width":"682","image_height":"960"}],"workflow_file":null,"grant_references":[],"version_history":[],"title":"Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import","principal_investigator":[{"author_orcid":"0000-0003-2580-4622","middle_name":null,"organization":"Department of Integrative Structural and Computational Biology, The Scripps Research Institute","street":"10550 N Torrey Pines Rd","town_or_city":"La Jolla","state_or_province":"California","post_or_zip":"92037","telephone":null,"fax":null,"first_name":"Ya-Ting","last_name":"Chang","email":"ychang [at] scripps.edu","country":"United States","entry":"EMPIAR-12534"}],"status":"REL","deposition_date":"2025-01-10","release_date":"2025-03-17","obsolete_date":null,"update_date":"2025-03-17","corresponding_author":{"author":{"author_orcid":"0000-0003-2580-4622","middle_name":null,"organization":"Department of Integrative Structural and Computational Biology, The Scripps Research Institute","street":"10550 N Torrey Pines Rd","town_or_city":"La Jolla","state_or_province":"California","post_or_zip":"92037","first_name":"Ya-Ting","last_name":"Chang","country":"United States"}},"authors":[{"author":{"name":"Chang YT","author_orcid":"0000-0003-2580-4622"}},{"author":{"name":"Barad BA","author_orcid":"0000-0002-1016-862X"}},{"author":{"name":"Rahmani H","author_orcid":"0000-0003-0222-6989"}},{"author":{"name":"Zid BM","author_orcid":"0000-0003-1876-2479"}},{"author":{"name":"Grotjahn DA","author_orcid":"0000-0001-5908-7882"}}],"cross_references":["EMD-48751","EMD-48752"],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Chang YT","author_orcid":"0000-0003-2580-4622"},{"name":"Barad BA","author_orcid":"0000-0002-1016-862X"},{"name":"Rahmani H","author_orcid":"0000-0003-0222-6989"},{"name":"Zid BM","author_orcid":"0000-0003-1876-2479"},{"name":"Grotjahn DA","author_orcid":"0000-0001-5908-7882"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import","volume":null,"country":"United States","first_page":null,"last_page":null,"year":"2024","language":"English","doi":"10.1101/2024.07.17.604013","pubmedid":"39071314","details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"bioRxiv","journal_abbreviation":"","issue":null,"preprint":true}],"dataset_size":"764.2 GB","experiment_type":"EMDB","scale":"cell","entry_doi":"10.6019/EMPIAR-12534"}}