{"EMPIAR-10062":{"imagesets":[{"segmentations":[],"name":"Tilt series of budding yeast cell cryosections and purified chromatin","directory":"data","category":"class averages","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":29,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":5.8,"pixel_height":5.8,"micrographs_file_pattern":null,"picked_particles_file_pattern":null,"picked_particles_directory":null,"details":"Tilt series data were acquired at various mags, resulting in either 5.8 or 8.9 Å pixel dimensions. Image width and height are variable.\n\n# Budding yeast chromatin is dispersed in a crowded nucleoplasm in vivo\n# Chen Chen, Hong Hwa Lim, Jian Shi, Sachiko Tamura, Kazuhiro Maeshima, Uttam Surana, Lu Gan\n#\n# IMOD reconstruction of yeast and chromatin cryotomograms\n#\n# Revised 20160417; IMOD version 4.8.47 3/17/2016\n# This dir contains the minimal number of files needed to reconstruct the tomograms in Chen et. al.\n# Note that some of the tomograms need to be binned x2 to facilitate visualization.\n1) Make a .st file from the .mrc tilt series and place in the correct dir (see details below).\n2) Run etomo from that directory:\n   etomo 14oct01a__014.edf\n3) In etomo, execute only the following commands.\n  Final Aligned Stack: (Create Tab) Create Full Aligned Stack\n                       (Correct CTF Tab) Select the right Falcon noise file, Correct CTF, Use CTF Correction\n                       (2D Filter Tab) Filter, Used Filtered Stack, Done\n  Tomogram Generation: Generate Tomogram, Done\n  Post-processing    : Trim Volume, Done\n  Clean Up           : optional cleanup, Done\n\nCreate .st files as follows:\n\n# The following use the Falcon2_20141217 noise files for CTF correction\nnewstack -secs 1-61 14oct01a__014.mrc 14oct01a__014.st\nnewstack -secs 0-47 14oct01a__021.mrc 14oct01a__021.st\nnewstack 14oct01a__027.mrc 14oct01a__027.st\nnewstack 14oct01a__032.mrc 14oct01a__032.st\nnewstack -secs 2-59 14oct01a__052.mrc 14oct01a__052.st\nnewstack -secs 0-60 14oct01a__067.mrc 14oct01a__067.st\n\n# The following use the Falcon2_20150328 noise files for CTF correction\nnewstack 15apr11_chrom_01.mrc chrom_01.st\nnewstack 15apr11_chrom_02.mrc chrom_02.st\nnewstack 15apr29_chrom_15.mrc chrom_15.st\nnewstack 15apr29_chrom_32.mrc chrom_32.st\nnewstack -secs 0-58 15mar02a__046.mrc 15mar02a__046.st\nnewstack 15mar02a__065.mrc 15mar02a__065.st\nnewstack 15mar02a__070.mrc 15mar02a__070.st\nnewstack -secs 0-59 15mar02a__074.mrc 15mar02a__074.st\nnewstack 15may05_chrom_07.mrc chrom_07.st\nnewstack 15may29_chrom_11.mrc chrom_11.st\nnewstack 15may29_chrom_15.mrc chrom_15.st\nnewstack 15may29_chrom_19.mrc chrom_19.st\nnewstack 15may29_chrom_21.mrc chrom_21.st\nnewstack 15oct12_yeast_02.mrc yeast_02.st\nnewstack 15oct12_yeast_03.mrc yeast_03.st\nnewstack 15oct12_yeast_04.mrc yeast_04.st\nnewstack 15oct12_yeast_12.mrc yeast_12.st\nnewstack 15oct12_yeast_15.mrc yeast_15.st\nnewstack 16jan29_yeast_01.mrc yeast_01.st\nnewstack 16jan29_yeast_05.mrc yeast_05.st\nnewstack 16jan29_yeast_09.mrc yeast_09.st\nnewstack 16jan29_yeast_10.mrc yeast_10.st\nnewstack 16jan29_yeast_17.mrc yeast_17.st","image_width":null,"image_height":null}],"workflow_file":null,"grant_references":[],"version_history":[],"title":"Electron cryotomography of cryosectioned budding yeast cells","principal_investigator":[{"author_orcid":"0000-0002-8685-4896","middle_name":null,"organization":"Centre for BioImaging Sciences, Dept. of Biological Sciences, National University of Singapore","street":"14 Science Drive 4","town_or_city":"Singapore","state_or_province":"Singapore","post_or_zip":"117543","telephone":null,"fax":null,"first_name":"Lu","last_name":"Gan","email":"lu [at] anaphase.org","country":"Singapore","entry":"EMPIAR-10062"}],"status":"REL","deposition_date":"2016-06-02","release_date":"2016-11-11","obsolete_date":null,"update_date":"2016-11-11","corresponding_author":{"author":{"author_orcid":"0000-0002-8685-4896","middle_name":null,"organization":"Centre for BioImaging Sciences, Dept. of Biological Sciences, National University of Singapore","street":"14 Science Drive 4","town_or_city":"Singapore","state_or_province":"Singapore","post_or_zip":"117543","first_name":"Lu","last_name":"Gan","country":"Singapore"}},"authors":[{"author":{"name":"Chen C","author_orcid":null}},{"author":{"name":"Lim HH","author_orcid":null}},{"author":{"name":"Shi J","author_orcid":null}},{"author":{"name":"Tamura S","author_orcid":null}},{"author":{"name":"Maeshima M","author_orcid":"0000-0003-3909-0341"}},{"author":{"name":"Surana U","author_orcid":null}},{"author":{"name":"Gan L","author_orcid":"0000-0002-8685-4896"}}],"cross_references":["EMD-8157"],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Chen C","author_orcid":null},{"name":"Lim HH","author_orcid":"0000-0002-0951-7220"},{"name":"Shi J","author_orcid":null},{"name":"Tamura S","author_orcid":null},{"name":"Maeshima K","author_orcid":null},{"name":"Surana U","author_orcid":null},{"name":"Gan L","author_orcid":"0000-0002-8685-4896"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Budding yeast chromatin is dispersed in a crowded nucleoplasm in vivo","volume":"27","country":"","first_page":"3357","last_page":"3368","year":"2016","language":"English","doi":"10.1091/mbc.E16-07-0506","pubmedid":"27605704","details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"Molecular biology of the cell","journal_abbreviation":"Mol. Biol. Cell","issue":"21","preprint":false}],"dataset_size":"125.3 GB","experiment_type":"EMDB","scale":null,"entry_doi":"10.6019/EMPIAR-10062"}}