[{"status":"public","ddc":["570"],"title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"_id":"11653","year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:35:53Z","date_created":"2022-07-26T11:01:47Z","file":[{"file_id":"11655","embargo":"2022-08-07","title":"Supplementary Datasets","relation":"main_file","date_updated":"2022-08-08T22:30:04Z","date_created":"2022-07-26T12:37:52Z","checksum":"5f1d7c6d7ab5375ed2564521432bed0c","file_name":"Data.zip","description":"The folder contains the following datasets (fasta files, and text files):\nSup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan\nmale draft assembly\nSup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana\nSup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and\nA. parthenogenetica females and rare male.\nSup. Dataset 4: Artemia sinica Male:female FST per 1Kb window\nSup. Dataset 5: FASTA file with candidate W scaffolds\nSup. Dataset 6: Candidate W-derived transcripts and alignments\nSup. Dataset 7: Gene expression with genomic location\nSup. Dataset 8: VCF for asexual female and rare male\nSup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)\nSup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using\nA. sp. Kazakhstan as the reference), and inferred ancestry\nSup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their\nlocations in the Artemia sinica male genome.\n","access_level":"open_access","creator":"melkrewi","content_type":"application/x-zip-compressed","file_size":2209382998}],"oa_version":"Published Version","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","first_name":"Marwan N","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N"}],"contributor":[{"orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","first_name":"Marwan N"},{"first_name":"Uladzislava","last_name":"Khauratovich"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","first_name":"Melissa A"},{"last_name":"Bett","first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac","first_name":"Andrea"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","first_name":"Ariana"},{"orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle"},{"last_name":"Sax","first_name":"Luca"},{"last_name":"Huylmans","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hontoria ","first_name":"Francisco"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"12248"}]},"type":"research_data","abstract":[{"lang":"eng","text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality."}],"file_date_updated":"2022-08-08T22:30:04Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"chicago":"Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:11653.","short":"M.N. Elkrewi, (2022).","mla":"Elkrewi, Marwan N. Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:11653.","ieee":"M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2022.","apa":"Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:11653","ista":"Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:11653.","ama":"Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:10.15479/AT:ISTA:11653"},"oa":1,"date_published":"2022-08-05T00:00:00Z","doi":"10.15479/AT:ISTA:11653","day":"05","month":"08","article_processing_charge":"No","has_accepted_license":"1"},{"author":[{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios"}],"date_created":"2021-03-27T13:47:49Z","date_updated":"2024-02-21T12:37:14Z","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"Raw Data- Enhancement of Superconductivity in a Planar Ge hole gas.zip","file_size":10616071,"content_type":"application/x-zip-compressed","creator":"gkatsaro","relation":"main_file","file_id":"9292","checksum":"635df3c08fc13c3dac008cd421aefbe4","success":1,"date_updated":"2021-03-27T13:46:17Z","date_created":"2021-03-27T13:46:17Z"},{"file_size":470,"content_type":"text/plain","creator":"dernst","file_name":"README.txt","access_level":"open_access","date_created":"2021-04-01T07:52:56Z","date_updated":"2021-04-01T07:52:56Z","checksum":"12b3ca69ae7509a346711baae0b02a75","success":1,"relation":"main_file","file_id":"9302"}],"_id":"9291","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","ddc":["530"],"status":"public","title":"Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium","department":[{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","abstract":[{"text":"This .zip File contains the transport data for figures presented in the main text and supplementary material of \"Enhancement of Proximity Induced Superconductivity in Planar Germanium\" by K. Aggarwal, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html).","lang":"eng"}],"file_date_updated":"2021-04-01T07:52:56Z","type":"research_data","date_published":"2021-03-29T00:00:00Z","doi":"10.15479/AT:ISTA:9291","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"ista":"Katsaros G. 2021. Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9291.","ieee":"G. Katsaros, “Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium.” Institute of Science and Technology Austria, 2021.","apa":"Katsaros, G. (2021). Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9291","ama":"Katsaros G. Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium. 2021. doi:10.15479/AT:ISTA:9291","chicago":"Katsaros, Georgios. “Raw Transport Data for: Enhancement of Proximity Induced Superconductivity in Planar Germanium.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9291.","mla":"Katsaros, Georgios. Raw Transport Data for: Enhancement of Proximity Induced Superconductivity in Planar Germanium. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9291.","short":"G. Katsaros, (2021)."},"day":"29","month":"03","has_accepted_license":"1","article_processing_charge":"No"},{"department":[{"_id":"AnHi"}],"publisher":"Institute of Science and Technology Austria","status":"public","title":"Data for \"Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid\"","year":"2021","_id":"9636","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"9637","date_updated":"2021-07-07T20:37:28Z","date_created":"2021-07-07T20:37:28Z","checksum":"18e90687ec7bbd75f8bfea4d8293fb30","success":1,"file_name":"figures_data.zip","access_level":"open_access","content_type":"application/zip","file_size":3345244,"creator":"ahigginb"}],"date_updated":"2024-02-21T12:36:52Z","date_created":"2021-07-07T20:43:10Z","related_material":{"record":[{"id":"10029","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","first_name":"Andrew P"}],"type":"research_data","file_date_updated":"2021-07-07T20:37:28Z","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"citation":{"chicago":"Higginbotham, Andrew P. “Data for ‘Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.’” Institute of Science and Technology Austria, 2021.","short":"A.P. Higginbotham, (2021).","mla":"Higginbotham, Andrew P. Data for “Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.” Institute of Science and Technology Austria, 2021.","apa":"Higginbotham, A. P. (2021). Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” Institute of Science and Technology Austria.","ieee":"A. P. Higginbotham, “Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.’” Institute of Science and Technology Austria, 2021.","ista":"Higginbotham AP. 2021. Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid’, Institute of Science and Technology Austria.","ama":"Higginbotham AP. Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” 2021."},"date_published":"2021-01-01T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1"},{"date_published":"2021-04-14T00:00:00Z","doi":"10.15479/AT:ISTA:9323","oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"short":"D. Jirovec, (2021).","mla":"Jirovec, Daniel. Research Data for “A Singlet-Triplet Hole Spin Qubit Planar Ge.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9323.","chicago":"Jirovec, Daniel. “Research Data for ‘A Singlet-Triplet Hole Spin Qubit Planar Ge.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9323.","ama":"Jirovec D. Research data for “A singlet-triplet hole spin qubit planar Ge.” 2021. doi:10.15479/AT:ISTA:9323","apa":"Jirovec, D. (2021). Research data for “A singlet-triplet hole spin qubit planar Ge.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9323","ieee":"D. Jirovec, “Research data for ‘A singlet-triplet hole spin qubit planar Ge.’” Institute of Science and Technology Austria, 2021.","ista":"Jirovec D. 2021. Research data for ‘A singlet-triplet hole spin qubit planar Ge’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9323."},"article_processing_charge":"No","has_accepted_license":"1","day":"14","month":"04","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"DataRepositorySTqubit.zip","file_size":221832287,"content_type":"application/x-zip-compressed","creator":"djirovec","relation":"main_file","file_id":"9324","checksum":"c569d2a2ce1694445cdbca19cf8ae023","success":1,"date_created":"2021-04-14T09:48:47Z","date_updated":"2021-04-14T09:48:47Z"},{"access_level":"open_access","file_name":"ReadMe","creator":"djirovec","content_type":"application/octet-stream","file_size":4323,"file_id":"9325","relation":"main_file","success":1,"checksum":"845bdf87430718ad6aff47eda7b5fc92","date_created":"2021-04-14T09:49:30Z","date_updated":"2021-04-14T09:49:30Z"}],"date_created":"2021-04-14T09:50:22Z","date_updated":"2024-02-21T12:39:15Z","contributor":[{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","contributor_type":"project_member","last_name":"Jirovec"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8909"}]},"author":[{"full_name":"Jirovec, Daniel","last_name":"Jirovec","first_name":"Daniel","orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"status":"public","ddc":["530"],"title":"Research data for \"A singlet-triplet hole spin qubit planar Ge\"","_id":"9323","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","abstract":[{"text":"This .zip File contains the data for figures presented in the main text and supplementary material of \"A singlet triplet hole spin qubit in planar Ge\" by D. Jirovec, et. al. The measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html). A single file is acquired with QCodes and features the corresponding data type. XRD data are in .dat format and a code to open the data is provided. The code for simulations is as well provided in Python.","lang":"eng"}],"file_date_updated":"2021-04-14T09:49:30Z","type":"research_data"},{"type":"research_data","abstract":[{"lang":"eng","text":"This .zip File contains the transport data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\" by M. Valentini, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format.\r\nInstructions of how to read the data are in \"Notebook_Valentini.pdf\"."}],"file_date_updated":"2021-05-14T11:56:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9389","year":"2021","status":"public","ddc":["530"],"title":"Research data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\"","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"author":[{"first_name":"Marco","last_name":"Valentini","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","full_name":"Valentini, Marco"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8910"}]},"contributor":[{"contributor_type":"contact_person","last_name":"Valentini","first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425"}],"date_updated":"2024-02-21T12:40:09Z","date_created":"2021-05-14T12:07:53Z","oa_version":"Published Version","file":[{"creator":"mvalenti","content_type":"application/pdf","file_size":10572981,"access_level":"open_access","file_name":"Notebook_Valentini.pdf","checksum":"80a905c4eef24dab6fb247e81a3d67f5","date_updated":"2021-05-14T11:42:23Z","date_created":"2021-05-14T11:42:23Z","file_id":"9390","relation":"main_file"},{"checksum":"1e61a7e63949448a8db0091cdac23570","date_updated":"2021-05-14T11:56:48Z","date_created":"2021-05-14T11:56:48Z","file_id":"9391","relation":"main_file","creator":"mvalenti","content_type":"application/x-zip-compressed","file_size":99076111,"access_level":"open_access","file_name":"Experimental_data.zip"}],"has_accepted_license":"1","article_processing_charge":"No","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"chicago":"Valentini, Marco. “Research Data for ‘Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9389.","short":"M. Valentini, (2021).","mla":"Valentini, Marco. Research Data for “Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9389.","ieee":"M. Valentini, “Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.’” Institute of Science and Technology Austria, 2021.","apa":"Valentini, M. (2021). Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9389","ista":"Valentini M. 2021. Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9389.","ama":"Valentini M. Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” 2021. doi:10.15479/AT:ISTA:9389"},"doi":"10.15479/AT:ISTA:9389","date_published":"2021-01-01T00:00:00Z","acknowledged_ssus":[{"_id":"NanoFab"}]},{"date_updated":"2024-02-21T12:41:09Z","date_created":"2021-02-24T17:49:21Z","file":[{"file_size":5934452,"content_type":"application/x-zip-compressed","creator":"larathoo","file_name":"Data_Code.zip","access_level":"open_access","date_created":"2021-02-24T17:45:13Z","date_updated":"2021-02-24T17:45:13Z","checksum":"f85537815809a8a4b7da9d01163f88c0","success":1,"relation":"main_file","file_id":"9193"}],"oa_version":"Published Version","author":[{"last_name":"Surendranadh","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","full_name":"Surendranadh, Parvathy"},{"full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","first_name":"Louise S"},{"full_name":"Baskett, Carina","last_name":"Baskett","first_name":"Carina","orcid":"0000-0002-7354-8574","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David"},{"full_name":"Pickup, Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"contributor":[{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh","contributor_type":"project_member","first_name":"Parvathy"},{"first_name":"Louise S","contributor_type":"project_member","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Baskett","contributor_type":"project_member","first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"project_member","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"project_member","last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","contributor_type":"project_leader"}],"related_material":{"record":[{"id":"11411","relation":"used_in_publication","status":"public"},{"relation":"later_version","status":"public","id":"11321"},{"id":"8254","status":"public","relation":"earlier_version"}]},"title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","status":"public","ddc":["576"],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","year":"2021","_id":"9192","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Here are the research data underlying the publication \" Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus).\" Further information are summed up in the README document.","lang":"eng"}],"file_date_updated":"2021-02-24T17:45:13Z","type":"research_data","date_published":"2021-02-26T00:00:00Z","doi":"10.15479/AT:ISTA:9192","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"citation":{"ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 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Enhancement of proximity induced superconductivity in planar Germanium, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8834.","ieee":"G. Katsaros, “Enhancement of proximity induced superconductivity in planar Germanium.” Institute of Science and Technology Austria, 2020.","apa":"Katsaros, G. (2020). Enhancement of proximity induced superconductivity in planar Germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8834","ama":"Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium. 2020. doi:10.15479/AT:ISTA:8834","chicago":"Katsaros, Georgios. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8834.","mla":"Katsaros, Georgios. Enhancement of Proximity Induced Superconductivity in Planar Germanium. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8834.","short":"G. Katsaros, (2020)."},"oa":1,"date_published":"2020-12-02T00:00:00Z","doi":"10.15479/AT:ISTA:8834"},{"doi":"10.15479/AT:ISTA:8097","date_published":"2020-07-15T00:00:00Z","acknowledged_ssus":[{"_id":"LifeSc"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"short":"B. Kavcic, (2020).","mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8097.","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8097.","ama":"Kavcic B. Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” 2020. doi:10.15479/AT:ISTA:8097","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8097","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics.’” Institute of Science and Technology Austria, 2020.","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8097."},"article_processing_charge":"No","has_accepted_license":"1","day":"15","month":"07","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"contributor":[{"contributor_type":"research_group","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tobias","last_name":"Bollenbach","contributor_type":"research_group","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"author":[{"full_name":"Kavcic, Bor","first_name":"Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X"}],"oa_version":"Published Version","file":[{"file_size":255770756,"content_type":"application/zip","creator":"bkavcic","access_level":"open_access","file_name":"natComm_2020_scripts.zip","checksum":"5c321dbbb6d4b3c85da786fd3ebbdc98","date_updated":"2020-07-14T12:48:09Z","date_created":"2020-07-06T20:38:27Z","relation":"main_file","file_id":"8098"}],"date_created":"2020-07-06T20:40:19Z","date_updated":"2024-02-21T12:40:51Z","year":"2020","_id":"8097","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"status":"public","title":"Analysis scripts and research data for the paper \"Mechanisms of drug interactions between translation-inhibiting antibiotics\"","file_date_updated":"2020-07-14T12:48:09Z","abstract":[{"text":"Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by \"translation bottlenecks\": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of \"continuous epistasis\" in bacterial physiology.","lang":"eng"}],"type":"research_data"},{"citation":{"chicago":"Arathoon, Louise S. “Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus).” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8254.","short":"L.S. Arathoon, (2020).","mla":"Arathoon, Louise S. Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus). Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8254.","ieee":"L. S. Arathoon, “Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus).” Institute of Science and Technology Austria, 2020.","apa":"Arathoon, L. S. (2020). Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8254","ista":"Arathoon LS. 2020. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus), Institute of Science and Technology Austria, 10.15479/AT:ISTA:8254.","ama":"Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:10.15479/AT:ISTA:8254"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"doi":"10.15479/AT:ISTA:8254","date_published":"2020-08-18T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","month":"08","day":"18","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","ddc":["576"],"title":"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)","status":"public","year":"2020","_id":"8254","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":5778420,"content_type":"application/x-zip-compressed","creator":"dernst","file_name":"Data_Rcode_MathematicaNB.zip","access_level":"open_access","date_updated":"2020-08-18T08:03:23Z","date_created":"2020-08-18T08:03:23Z","checksum":"4f1382ed4384751b6013398c11557bf6","success":1,"relation":"main_file","file_id":"8280"}],"oa_version":"Published Version","date_updated":"2024-02-21T12:41:09Z","date_created":"2020-08-12T12:49:23Z","contributor":[{"first_name":"Louise S","contributor_type":"data_collector","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Surendranadh","contributor_type":"project_member","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Barton","first_name":"Nicholas H"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field","contributor_type":"project_member"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","contributor_type":"project_member","last_name":"Pickup"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","contributor_type":"project_member","last_name":"Baskett"}],"related_material":{"record":[{"id":"11321","relation":"later_version","status":"public"},{"status":"public","relation":"later_version","id":"9192"}]},"author":[{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1771-714X","first_name":"Louise S","last_name":"Arathoon","full_name":"Arathoon, Louise S"}],"type":"research_data","abstract":[{"text":"Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192.","lang":"eng"}],"file_date_updated":"2020-08-18T08:03:23Z"},{"type":"research_data","abstract":[{"text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.","lang":"eng"}],"file_date_updated":"2020-12-09T15:00:19Z","_id":"8930","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","department":[{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","ddc":["570"],"status":"public","related_material":{"record":[{"id":"8997","relation":"used_in_publication","status":"public"}]},"contributor":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","contributor_type":"supervisor","last_name":"Tkačik"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bollenbach","contributor_type":"supervisor"}],"author":[{"full_name":"Kavcic, Bor","last_name":"Kavcic","first_name":"Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"}],"file":[{"date_updated":"2020-12-09T15:00:19Z","date_created":"2020-12-09T15:00:19Z","success":1,"checksum":"60a818edeffaa7da1ebf5f8fbea9ba18","file_id":"8932","relation":"main_file","creator":"bkavcic","file_size":315494370,"content_type":"application/zip","file_name":"PLoSCompBiol2020_datarep.zip","access_level":"open_access"}],"oa_version":"Published Version","date_created":"2020-12-09T15:04:02Z","date_updated":"2024-02-21T12:41:42Z","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"has_accepted_license":"1","article_processing_charge":"No","month":"12","day":"10","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"ama":"Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:10.15479/AT:ISTA:8930","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8930","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020.","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8930.","short":"B. Kavcic, (2020).","mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8930.","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8930."},"date_published":"2020-12-10T00:00:00Z","doi":"10.15479/AT:ISTA:8930"},{"department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","status":"public","ddc":["570"],"title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","_id":"8951","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"8952","relation":"main_file","success":1,"checksum":"f57862aeee1690c7effd2b1117d40ed1","date_created":"2020-12-20T09:52:52Z","date_updated":"2020-12-20T09:52:52Z","access_level":"open_access","file_name":"readme.txt","creator":"bkavcic","content_type":"text/plain","file_size":523},{"creator":"bkavcic","file_size":379228,"content_type":"application/octet-stream","file_name":"GRNs Research depository.gb","access_level":"open_access","date_updated":"2020-12-20T22:01:44Z","date_created":"2020-12-20T22:01:44Z","success":1,"checksum":"f2c6d5232ec6d551b6993991e8689e9f","file_id":"8954","relation":"main_file"}],"date_created":"2020-12-20T10:00:26Z","date_updated":"2024-02-21T12:41:57Z","related_material":{"record":[{"id":"9283","status":"public","relation":"used_in_publication"}]},"contributor":[{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A","contributor_type":"project_member","last_name":"Nagy-Staron"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin","last_name":"Tomasek","contributor_type":"project_member"},{"first_name":"Caroline","last_name":"Caruso Carter","contributor_type":"project_member"},{"first_name":"Elisabeth","contributor_type":"project_member","last_name":"Sonnleitner"},{"orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Kavcic","first_name":"Bor"},{"first_name":"Tiago","last_name":"Paixão","contributor_type":"project_member"},{"first_name":"Calin C","last_name":"Guet","contributor_type":"project_manager","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"}],"author":[{"first_name":"Anna A","last_name":"Nagy-Staron","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1391-8377","full_name":"Nagy-Staron, Anna A"}],"type":"research_data","abstract":[{"lang":"eng","text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks."}],"file_date_updated":"2020-12-20T22:01:44Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:10.15479/AT:ISTA:8951","ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8951.","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8951","mla":"Nagy-Staron, Anna A. Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8951.","short":"A.A. Nagy-Staron, (2020).","chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8951."},"doi":"10.15479/AT:ISTA:8951","date_published":"2020-12-21T00:00:00Z","keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"article_processing_charge":"No","has_accepted_license":"1","day":"21","month":"12"},{"has_accepted_license":"1","article_processing_charge":"No","day":"28","month":"01","keyword":["Matlab scripts","analysis of microfluidics","mathematical model"],"date_published":"2020-01-28T00:00:00Z","doi":"10.15479/AT:ISTA:7383","citation":{"chicago":"Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7383.","short":"R. Grah, (2020).","mla":"Grah, Rok. Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7383.","ieee":"R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020.","apa":"Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7383","ista":"Grah R. 2020. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7383.","ama":"Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:10.15479/AT:ISTA:7383"},"oa":1,"abstract":[{"lang":"eng","text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. 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Supplementary Data for “Computational Design of Cold Bent Glass Façades.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8761.","short":"R. Guseinov, (2020).","chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Computational Design of Cold Bent Glass Façades.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8761.","ama":"Guseinov R. Supplementary data for “Computational design of cold bent glass façades.” 2020. doi:10.15479/AT:ISTA:8761","ista":"Guseinov R. 2020. Supplementary data for ‘Computational design of cold bent glass façades’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8761.","ieee":"R. Guseinov, “Supplementary data for ‘Computational design of cold bent glass façades.’” Institute of Science and Technology Austria, 2020.","apa":"Guseinov, R. (2020). Supplementary data for “Computational design of cold bent glass façades.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8761"},"oa":1},{"abstract":[{"text":"Supplementary data provided for the provided for the publication:\r\nIgor Gridchyn , Philipp Schoenenberger , Joseph O'Neill , Jozsef Csicsvari (2020) Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. 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Csicsvari, I. Gridchyn, P. Schönenberger, (2020).","mla":"Csicsvari, Jozsef L., et al. Optogenetic Alteration of Hippocampal Network Activity. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8563.","ieee":"J. L. Csicsvari, I. Gridchyn, and P. Schönenberger, “Optogenetic alteration of hippocampal network activity.” Institute of Science and Technology Austria, 2020.","apa":"Csicsvari, J. L., Gridchyn, I., & Schönenberger, P. (2020). Optogenetic alteration of hippocampal network activity. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8563","ista":"Csicsvari JL, Gridchyn I, Schönenberger P. 2020. Optogenetic alteration of hippocampal network activity, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8563.","ama":"Csicsvari JL, Gridchyn I, Schönenberger P. Optogenetic alteration of hippocampal network activity. 2020. doi:10.15479/AT:ISTA:8563"},"oa":1},{"abstract":[{"text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications.","lang":"eng"}],"file_date_updated":"2023-12-01T10:39:59Z","type":"research_data","author":[{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM"}],"contributor":[{"first_name":"Florian","last_name":"Fäßler","contributor_type":"researcher","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X"},{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","contributor_type":"researcher","last_name":"Zens"},{"contributor_type":"researcher","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schur","contributor_type":"researcher","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"8586","status":"public","relation":"research_data"}]},"date_updated":"2024-02-21T12:44:48Z","date_created":"2023-11-22T15:00:57Z","file":[{"relation":"main_file","file_id":"14593","checksum":"0108616e2a59e51879ea51299a29b091","success":1,"date_updated":"2023-11-22T14:58:44Z","date_created":"2023-11-22T14:58:44Z","access_level":"open_access","file_name":"3Dprint-files_download_v2.zip","file_size":49297,"content_type":"application/zip","creator":"fschur"},{"relation":"main_file","file_id":"14637","checksum":"4c66ddedee4d01c1c4a7978208350cfc","success":1,"date_updated":"2023-12-01T10:39:59Z","date_created":"2023-12-01T10:39:59Z","access_level":"open_access","file_name":"readme.txt","content_type":"text/plain","file_size":641,"creator":"cchlebak"}],"oa_version":"Published Version","_id":"14592","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"status":"public","title":"STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","publisher":"Institute of Science and Technology Austria","department":[{"_id":"FlSc"}],"day":"01","month":"12","article_processing_charge":"No","has_accepted_license":"1","date_published":"2020-12-01T00:00:00Z","doi":"10.15479/AT:ISTA:14592","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"citation":{"ama":"Schur FK. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. 2020. doi:10.15479/AT:ISTA:14592","ista":"Schur FK. 2020. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14592.","ieee":"F. K. Schur, “STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy.” Institute of Science and Technology Austria, 2020.","apa":"Schur, F. K. (2020). STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14592","mla":"Schur, Florian KM. STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:14592.","short":"F.K. Schur, (2020).","chicago":"Schur, Florian KM. “STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:14592."},"oa":1,"project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"}]},{"department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","status":"public","title":"Data for the paper \"Gene amplification as a form of population-level gene expression regulation\"","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7016","year":"2019","file":[{"creator":"itomanek","file_size":2456192500,"content_type":"application/octet-stream","access_level":"open_access","description":"Illumina whole genome sequence data for Locus 1 - amplified.","file_name":"D8_S35_R2_001.fastq","checksum":"72441055043eda4cbf1398a422e2c118","date_created":"2019-11-13T08:52:21Z","date_updated":"2020-07-14T12:47:47Z","file_id":"7017","title":"Locus1_amplified","relation":"main_file"},{"file_size":2833452234,"content_type":"application/octet-stream","creator":"itomanek","access_level":"open_access","file_name":"IT028_S11_R2_001.fastq","description":"Illumina whole genome sequence data for Locus 1 - 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see read_me_FACS","file_name":"FACS_data.xlsx.zip","access_level":"open_access","content_type":"application/zip","file_size":3765861,"creator":"itomanek"},{"file_name":"read_me_FACS.rtf","access_level":"open_access","content_type":"text/rtf","file_size":4996,"creator":"itomanek","relation":"main_file","file_id":"7352","date_updated":"2020-07-14T12:47:47Z","date_created":"2020-01-22T15:44:16Z","checksum":"a85caf092ae4b17668f70af2d93fad00"},{"checksum":"fd8ba5d75d24e47ddf7e70bfdadb40d4","date_created":"2020-01-22T15:44:16Z","date_updated":"2020-07-14T12:47:47Z","relation":"main_file","file_id":"7353","file_size":868,"content_type":"text/rtf","creator":"itomanek","access_level":"open_access","file_name":"read_me_microfluidics.rtf"},{"creator":"itomanek","content_type":"application/zip","file_size":8141727,"file_name":"microfuidics_data.zip","description":"microfluidics time trace data - see read_me_microfluidics","access_level":"open_access","date_updated":"2020-07-14T12:47:47Z","date_created":"2020-01-22T15:44:17Z","checksum":"69c5dc5ca5c069a138183c934acc1778","file_id":"7354","title":"microfluidics data","relation":"main_file"}],"oa_version":"Published Version","date_created":"2019-11-13T09:07:31Z","date_updated":"2024-02-21T12:45:25Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7652"}]},"contributor":[{"last_name":"Guet","contributor_type":"project_leader","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"author":[{"full_name":"Tomanek, Isabella","first_name":"Isabella","last_name":"Tomanek","id":"3981F020-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6197-363X"}],"type":"research_data","abstract":[{"lang":"eng","text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature."}],"file_date_updated":"2020-07-14T12:47:47Z","citation":{"ama":"Tomanek I. Data for the paper “Gene amplification as a form of population-level gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016","ista":"Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level gene expression regulation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7016.","ieee":"I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level gene expression regulation.’” Institute of Science and Technology Austria, 2019.","apa":"Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level gene expression regulation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7016","mla":"Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7016.","short":"I. Tomanek, (2019).","chicago":"Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016."},"oa":1,"doi":"10.15479/AT:ISTA:7016","date_published":"2019-11-13T00:00:00Z","keyword":["Escherichia coli","gene amplification","galactose","DOG","experimental evolution","Illumina sequence data","FACS data","microfluidics data"],"article_processing_charge":"No","has_accepted_license":"1","day":"13","month":"11"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7154","year":"2019","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeBi"}],"title":"Supplementary data for \"Programming temporal morphing of self-actuated shells\"","status":"public","ddc":["000"],"related_material":{"record":[{"relation":"used_in_publication","status":"deleted","id":"8433"},{"id":"7262","status":"public","relation":"used_in_publication"}]},"contributor":[{"orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","last_name":"Guseinov","first_name":"Ruslan"},{"first_name":"Connor","last_name":"McMahan"},{"last_name":"Perez Rodriguez","first_name":"Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Daraio","first_name":"Chiara"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"}],"author":[{"full_name":"Guseinov, Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077","first_name":"Ruslan","last_name":"Guseinov"}],"file":[{"creator":"dernst","file_size":65307107,"content_type":"application/x-zip-compressed","access_level":"open_access","file_name":"temporal_morphing_supp_data.zip","checksum":"155133e6e188e85b3c0676a5e70b9341","date_updated":"2020-07-14T12:47:50Z","date_created":"2019-12-09T07:52:17Z","file_id":"7155","relation":"main_file"}],"oa_version":"Published Version","date_created":"2019-12-09T07:52:46Z","date_updated":"2024-02-21T12:45:03Z","type":"research_data","ec_funded":1,"file_date_updated":"2020-07-14T12:47:50Z","citation":{"chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Programming Temporal Morphing of Self-Actuated Shells.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7154.","mla":"Guseinov, Ruslan. Supplementary Data for “Programming Temporal Morphing of Self-Actuated Shells.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7154.","short":"R. Guseinov, (2019).","ista":"Guseinov R. 2019. Supplementary data for ‘Programming temporal morphing of self-actuated shells’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7154.","ieee":"R. Guseinov, “Supplementary data for ‘Programming temporal morphing of self-actuated shells.’” Institute of Science and Technology Austria, 2019.","apa":"Guseinov, R. (2019). Supplementary data for “Programming temporal morphing of self-actuated shells.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7154","ama":"Guseinov R. Supplementary data for “Programming temporal morphing of self-actuated shells.” 2019. doi:10.15479/AT:ISTA:7154"},"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"doi":"10.15479/AT:ISTA:7154","date_published":"2019-12-06T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","month":"12","day":"06"},{"doi":"10.15479/AT:ISTA:6060","date_published":"2019-02-28T00:00:00Z","oa":1,"citation":{"ama":"Vicoso B. Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . 2019. doi:10.15479/AT:ISTA:6060","ista":"Vicoso B. 2019. Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). , Institute of Science and Technology Austria, 10.15479/AT:ISTA:6060.","apa":"Vicoso, B. (2019). Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6060","ieee":"B. Vicoso, “Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). .” Institute of Science and Technology Austria, 2019.","mla":"Vicoso, Beatriz. Supplementary Data for “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome” (Huylman, Toups et Al., 2019). . Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6060.","short":"B. Vicoso, (2019).","chicago":"Vicoso, Beatriz. “Supplementary Data for ‘Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome’ (Huylman, Toups et Al., 2019). .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6060."},"day":"28","month":"02","article_processing_charge":"No","has_accepted_license":"1","date_created":"2019-02-28T10:55:15Z","date_updated":"2024-02-21T12:45:42Z","oa_version":"Published Version","file":[{"file_id":"6061","relation":"main_file","checksum":"a338a622d728af0e3199cb07e6dd64d3","date_created":"2019-02-28T10:54:27Z","date_updated":"2020-07-14T12:47:17Z","access_level":"open_access","file_name":"SupData.zip","creator":"bvicoso","content_type":"application/zip","file_size":36646050}],"author":[{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"related_material":{"record":[{"id":"6418","relation":"research_paper","status":"public"}]},"title":"Supplementary data for \"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome\" (Huylman, Toups et al., 2019). ","status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeVi"}],"_id":"6060","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","file_date_updated":"2020-07-14T12:47:17Z","type":"research_data"},{"doi":"10.15479/AT:ISTA:6074","date_published":"2019-01-09T00:00:00Z","oa":1,"citation":{"chicago":"Dotter, Christoph, and Gaia Novarino. “Supplementary Data for the Research Paper ‘Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6074.","mla":"Dotter, Christoph, and Gaia Novarino. Supplementary Data for the Research Paper “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6074.","short":"C. Dotter, G. Novarino, (2019).","ista":"Dotter C, Novarino G. 2019. Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6074.","apa":"Dotter, C., & Novarino, G. (2019). Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6074","ieee":"C. Dotter and G. Novarino, “Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.’” Institute of Science and Technology Austria, 2019.","ama":"Dotter C, Novarino G. Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” 2019. doi:10.15479/AT:ISTA:6074"},"day":"09","month":"01","has_accepted_license":"1","article_processing_charge":"No","author":[{"full_name":"Dotter, Christoph","last_name":"Dotter","first_name":"Christoph","orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia"}],"related_material":{"record":[{"id":"3","relation":"research_paper","status":"public"}]},"date_created":"2019-03-07T13:32:35Z","date_updated":"2024-02-21T13:41:01Z","oa_version":"Published Version","file":[{"relation":"supplementary_material","file_id":"6084","date_created":"2019-03-07T13:37:19Z","date_updated":"2020-07-14T12:47:18Z","checksum":"bc1b285edca9e98a2c63d153c79bb75b","file_name":"Setd5_paper.zip","access_level":"open_access","content_type":"application/zip","file_size":33202743,"creator":"dernst"}],"year":"2019","_id":"6074","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["570"],"title":"Supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\"","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaNo"}],"file_date_updated":"2020-07-14T12:47:18Z","abstract":[{"lang":"eng","text":"This dataset contains the supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\".\r\n\r\nThe contained files have the following content:\r\n'Supplementary Figures.pdf'\r\n\tAdditional figures (as referenced in the paper).\r\n'Supplementary Table 1. Statistics.xlsx'\r\n\tDetails on statistical tests performed in the paper.\r\n'Supplementary Table 2. Differentially expressed gene analysis.xlsx'\r\n\tResults for the differential gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro (ESCs, EBs, NPCs; analysis with DESeq2) samples.\r\n'Supplementary Table 3. Gene Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro (GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro samples were split into upregulated and downregulated genes (up/down) and the analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults for the differential gene expression analysis for samples from adult mice before (HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively). Each sheet shows the results for a different comparison. Sheets 1-3 show results for comparisons between timepoints for wild type (WT) samples only and sheets 4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results for comparisons between genotypes at each time point and sheet 10 contains the results for the analysis of differential expression trajectories between wild type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults for k-means clustering of genes by expression. Sheet 1 shows clustering of just the genes with significantly different expression trajectories between genotypes. Sheet 2 shows clustering of all genes that are significantly differentially expressed in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment analysis and EWCE analysis for enrichment of cell type specific genes for each cluster identified by clustering genes with different expression trajectories (see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet 1 shows protein protein interaction data generated from these results (combined with data from the STRING database. Sheet 2 shows the results of the statistical analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults for the Chip-Seq analysis for binding of RNA polymerase II (PolII). 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Performance under different mating scenarios.\r\n2. Comparison with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone."}],"file_date_updated":"2020-07-14T12:47:07Z"},{"author":[{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","first_name":"Tobias","last_name":"Bergmiller","full_name":"Bergmiller, Tobias"},{"full_name":"Nikolic, Nela","last_name":"Nikolic","first_name":"Nela","orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"research_paper","id":"438"}]},"date_updated":"2024-02-21T13:44:45Z","date_created":"2018-12-12T12:31:35Z","oa_version":"Published Version","file":[{"file_size":3558703796,"content_type":"application/zip","creator":"system","file_name":"IST-2018-74-v1+2_15-11-05.zip","access_level":"open_access","date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T13:04:39Z","checksum":"61ebb92213cfffeba3ddbaff984b81af","relation":"main_file","file_id":"5637"},{"relation":"main_file","file_id":"5638","date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T13:04:55Z","checksum":"bf26649af310ef6892d68576515cde6d","file_name":"IST-2018-74-v1+3_15-07-31.zip","access_level":"open_access","file_size":1830422606,"content_type":"application/zip","creator":"system"},{"file_name":"IST-2018-74-v1+4_Images_for_analysis.zip","access_level":"open_access","creator":"system","content_type":"application/zip","file_size":2140849248,"file_id":"5639","relation":"main_file","date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T13:05:11Z","checksum":"8e46eedce06f22acb2be1a9b9d3f56bd"}],"year":"2018","_id":"5569","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["579"],"title":"Time-lapse microscopy data","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:47:04Z","abstract":[{"text":"Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese, Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic.","lang":"eng"}],"publist_id":"7385","datarep_id":"74","type":"research_data","date_published":"2018-02-07T00:00:00Z","doi":"10.15479/AT:ISTA:74","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"mla":"Bergmiller, Tobias, and Nela Nikolic. Time-Lapse Microscopy Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:74.","short":"T. Bergmiller, N. Nikolic, (2018).","chicago":"Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:74.","ama":"Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:10.15479/AT:ISTA:74","ista":"Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science and Technology Austria, 10.15479/AT:ISTA:74.","ieee":"T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 2018.","apa":"Bergmiller, T., & Nikolic, N. (2018). Time-lapse microscopy data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:74"},"month":"02","day":"07","has_accepted_license":"1","article_processing_charge":"No","keyword":["microscopy","microfluidics"]},{"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"ieee":"D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018.","apa":"De Martino, D., & Tkačik, G. (2018). Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:62","ista":"De Martino D, Tkačik G. 2018. Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:62.","ama":"De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:10.15479/AT:ISTA:62","chicago":"De Martino, Daniele, and Gašper Tkačik. “Supporting Materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:62.","short":"D. De Martino, G. Tkačik, (2018).","mla":"De Martino, Daniele, and Gašper Tkačik. Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:62."},"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"}],"date_published":"2018-09-21T00:00:00Z","doi":"10.15479/AT:ISTA:62","keyword":["metabolic networks","e.coli core","maximum entropy","monte carlo markov chain sampling","ellipsoidal rounding"],"has_accepted_license":"1","article_processing_charge":"No","month":"09","day":"21","year":"2018","_id":"5587","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","ddc":["530"],"status":"public","related_material":{"record":[{"relation":"research_paper","status":"public","id":"161"}]},"author":[{"full_name":"De Martino, Daniele","last_name":"De Martino","first_name":"Daniele","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper"}],"file":[{"date_updated":"2020-07-14T12:47:08Z","date_created":"2018-12-12T13:05:13Z","checksum":"97992e3e8cf8544ec985a48971708726","relation":"main_file","file_id":"5641","file_size":14376,"content_type":"application/zip","creator":"system","file_name":"IST-2018-111-v1+1_CODES.zip","access_level":"open_access"}],"oa_version":"Published Version","date_updated":"2024-02-21T13:45:39Z","date_created":"2018-12-12T12:31:41Z","type":"research_data","datarep_id":"111","ec_funded":1,"file_date_updated":"2020-07-14T12:47:08Z","abstract":[{"lang":"eng","text":"Supporting material to the article \r\nSTATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\r\n\r\nboundscoli.dat\r\nFlux Bounds of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium. \r\n\r\npolcoli.dat\r\nMatrix enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium, \r\nobtained from the soichiometric matrix by standard linear algebra (reduced row echelon form).\r\n\r\nellis.dat\r\nApproximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\npoint0.dat\r\nCenter of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\nlovasz.cpp \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding the polytope\r\nwith the Lovasz method \r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015).\r\n\r\nsampleHRnew.cpp \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), the ellipsoid rounding the polytope, a point inside and \r\nit gives in output a max entropy sampling at fixed average growth rate \r\nof the steady states by performing an Hit-and-Run Monte Carlo Markov chain.\r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015)."}]},{"ec_funded":1,"file_date_updated":"2020-07-14T12:47:11Z","abstract":[{"text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants.","lang":"eng"}],"type":"research_data","related_material":{"record":[{"status":"public","relation":"research_paper","id":"6089"}]},"contributor":[{"last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Puixeu Sala","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle"}],"file":[{"checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:52Z","file_id":"5758","relation":"main_file","creator":"cfraisse","file_size":369837892,"content_type":"application/zip","access_level":"open_access","file_name":"FileS1.zip"},{"content_type":"application/zip","file_size":84856909,"creator":"cfraisse","access_level":"open_access","file_name":"FileS2.zip","checksum":"3592e467b4d8206650860b612d6e12f3","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:49Z","relation":"main_file","file_id":"5759"},{"file_id":"5760","relation":"main_file","checksum":"c37ac5d5437c457338afc128c1240655","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:49Z","access_level":"open_access","file_name":"FileS3.txt","creator":"cfraisse","content_type":"text/plain","file_size":881133},{"date_created":"2018-12-19T14:19:49Z","date_updated":"2020-07-14T12:47:11Z","checksum":"943dfd14da61817441e33e3e3cb8cdb9","relation":"main_file","file_id":"5761","file_size":883742,"content_type":"text/plain","creator":"cfraisse","file_name":"FileS4.txt","access_level":"open_access"},{"file_name":"FileS5.txt","access_level":"open_access","creator":"cfraisse","file_size":2495437,"content_type":"text/plain","file_id":"5762","relation":"main_file","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:49Z","checksum":"1c669b6c4690ec1bbca3e2da9f566d17"},{"creator":"cfraisse","content_type":"text/plain","file_size":15913457,"file_name":"FileS6.txt","access_level":"open_access","date_created":"2018-12-19T14:19:50Z","date_updated":"2020-07-14T12:47:11Z","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","file_id":"5763","relation":"main_file"},{"creator":"cfraisse","file_size":2584120,"content_type":"text/plain","file_name":"FileS7.txt","access_level":"open_access","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","file_id":"5764","relation":"main_file"},{"checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","date_created":"2018-12-19T14:19:50Z","date_updated":"2020-07-14T12:47:11Z","file_id":"5765","relation":"main_file","creator":"cfraisse","content_type":"text/plain","file_size":2446059,"access_level":"open_access","file_name":"FileS8.txt"},{"content_type":"text/plain","file_size":100737,"creator":"cfraisse","access_level":"open_access","file_name":"FileS9.txt","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","relation":"main_file","file_id":"5766"}],"oa_version":"Published Version","date_updated":"2024-02-21T13:59:18Z","date_created":"2018-12-19T14:22:35Z","_id":"5757","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"status":"public","title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","ddc":["576"],"has_accepted_license":"1","article_processing_charge":"No","day":"19","month":"12","keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"doi":"10.15479/at:ista:/5757","date_published":"2018-12-19T00:00:00Z","oa":1,"citation":{"apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:/5757","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018.","ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, 10.15479/at:ista:/5757.","ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:10.15479/at:ista:/5757","chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:/5757.","short":"C. Fraisse, (2018).","mla":"Fraisse, Christelle. Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:/5757."},"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"month":"07","day":"20","has_accepted_license":"1","article_processing_charge":"No","date_published":"2018-07-20T00:00:00Z","doi":"10.15479/AT:ISTA:108","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020"},{"grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425","name":"Design principles underlying genetic switch architecture (DOC Fellowship)"}],"oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:108.","mla":"Igler, Claudia, et al. 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It consists of preprocessed multi-electrode array recording from 160 salamander retinal ganglion cells responding to 297 repeats of a 19 s natural movie. The data is available in two formats: (1) a .mat file containing an array with dimensions “number of repeats” x “number of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data represented as an array with dimensions “number of neurons” x “number of samples”, where the number of samples is equal to the product of the number of repeats and timebins within a repeat. The time dimension is divided into 20 ms time windows, and the array is binary indicating whether a given cell elicited at least one spike in a given time window during a particular repeat. See the reference below for details regarding collection and preprocessing:\r\n\r\n[1] Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior in a Large Network of Sensory Neurons. 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