| session |
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data from Dyballa group"', 'type': 'dataset', 'extras': [{'key': 'contributor', 'value': 'Rieg, Carolin'}, {'key': 'creator', 'value': 'Dyballa, Michael'}, {'key': 'date', 'value': '2021-03-09T00:00:00'}, {'key': 'identifier', 'value': 'https://doi.org/10.18419/darus-1333'}, {'key': 'metadata_modified', 'value': '2022-11-29T01:00:03'}, {'key': 'set_spec', 'value': 'all'}, {'key': 'harvest_object_id', 'value': 'f74a5be5-97ff-43dc-994c-fc09c1d2dbdb'}, {'key': 'harvest_source_id', 'value': '8ba5ef26-d024-46cd-8099-94f1e74e7a36'}, {'key': 'harvest_source_title', 'value': 'Darus Test Harvest'}], 'resources': [{'cache_last_updated': None, 'cache_url': None, 'created': '2023-05-08T19:12:27.105146', 'format': 'HTML', 'hash': '', 'id': 'e840808f-8a9a-4eb1-865c-07a0a882856c', 'last_modified': None, 'metadata_modified': '2023-05-08T19:12:27.098508', 'mimetype': None, 'mimetype_inner': None, 'name': 'Publication data for: "Potential of triphenylphosphine as solid-state NMR probe for studying the noble metal distribution on porous supports - 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This Dataset contains the measurement results from ICP-OES , N2-Physisorption, MAS-NMR and TGA-DSC. The data are sorted by the position in the article (Table 1, Table 2 and so on). The NMR data (.dx-file) can be opened with TopSpin software.', 'num_resources': 1, 'num_tags': 1, 'organization': {'id': '9a7d2a53-21f6-412a-afb9-a15122df0640', 'name': 'darus', 'title': 'DaRUS', 'type': 'repository', 'description': 'Chemistry collection from DaRUS, the data repository of the University of Stuttgart.', 'image_url': 'logoDarusKreis.png', 'created': '2023-05-03T09:01:04.791551', 'is_organization': True, 'approval_status': 'approved', 'state': 'active'}, 'owner_org': '9a7d2a53-21f6-412a-afb9-a15122df0640', 'private': False, 'related_molecule': [], 'state': 'active', 'title': 'Publication data for: "Effect of aluminum and sodium on the sorption of water and methanol in microporous MFI-type zeolites and mesoporous SBA-15 materials" - data from Dyballa group', 'type': 'dataset', 'extras': [{'key': 'contributor', 'value': 'Li, Zheng'}, {'key': 'creator', 'value': 'Li, Zheng'}, {'key': 'date', 'value': '2021-04-12T00:00:00'}, {'key': 'identifier', 'value': 'https://doi.org/10.18419/darus-1332'}, {'key': 'metadata_modified', 'value': '2022-11-29T01:00:03'}, {'key': 'set_spec', 'value': 'all'}, {'key': 'harvest_object_id', 'value': '93db0c44-3d72-4d8f-94e3-47a9fb96eb4f'}, {'key': 'harvest_source_id', 'value': '8ba5ef26-d024-46cd-8099-94f1e74e7a36'}, {'key': 'harvest_source_title', 'value': 'Darus Test Harvest'}], 'resources': [{'cache_last_updated': None, 'cache_url': None, 'created': '2023-05-08T19:12:26.799764', 'format': 'HTML', 'hash': '', 'id': '89984148-18e9-440d-b700-45a033762bfa', 'last_modified': None, 'metadata_modified': '2023-05-08T19:12:26.793977', 'mimetype': None, 'mimetype_inner': None, 'name': 'Publication data for: "Effect of aluminum and sodium on the sorption of water and methanol in microporous MFI-type zeolites and mesoporous SBA-15 materials" - data from Dyballa group', 'package_id': 'doi-10-18419-darus-1332', 'position': 0, 'resource_type': 'HTML', 'size': None, 'state': 'active', 'url': 'https://doi.org/10.18419/darus-1332', 'url_type': None}], 'tags': [{'display_name': 'chemistry', 'id': '20e4e978-2a22-4286-a18b-4ae22d1ffca1', 'name': 'chemistry', 'state': 'active', 'vocabulary_id': None}], 'groups': [], 'relationships_as_subject': [], 'relationships_as_object': []}, {'author': 'Rieg, Carolin', 'author_email': None, 'creator_user_id': '1be646ae-ab26-47b8-8835-e4b27f11961e', 'id': 'doi-10-18419-darus-1326', 'isopen': False, 'license_id': '', 'license_title': '', 'maintainer': 'DaRUS', 'maintainer_email': None, 'metadata_created': '2023-05-08T19:12:26.490765', 'metadata_modified': '2023-05-08T19:12:26.490770', 'name': 'doi-10-18419-darus-1326', 'notes': 'All primary data files and processed data of the journal article from Dyballa group. \nThe uploaded data are sorted by the method of measurement, ICP-OES (inductively coupled plasma optical emission spectrometry), N2-Physisorption (BET), and MAS-NMR. NMR files are uploaded as jcampdx data and were processed with MestReNova. Also, SEM (scanning electron microscopy) images are uploaded. For the NMR data, the name of the corresponding figure is given, the figures SX can be found in the supporting information. The additional information "parent" signifies that the materials are not modified and desilicated. The desilicated materials with the end "DeSi" are mesoporous.', 'num_resources': 1, 'num_tags': 3, 'organization': {'id': '9a7d2a53-21f6-412a-afb9-a15122df0640', 'name': 'darus', 'title': 'DaRUS', 'type': 'repository', 'description': 'Chemistry collection from DaRUS, the data repository of the University of Stuttgart.', 'image_url': 'logoDarusKreis.png', 'created': '2023-05-03T09:01:04.791551', 'is_organization': True, 'approval_status': 'approved', 'state': 'active'}, 'owner_org': '9a7d2a53-21f6-412a-afb9-a15122df0640', 'private': False, 'related_molecule': [], 'state': 'active', 'title': 'Publication data for: "A Method for the Selective Quantification of Bronsted Acid Sites on External Surfaces and in Mesopores of Hierarchical Zeolites" - data from Dyballa group', 'type': 'dataset', 'extras': [{'key': 'contributor', 'value': 'Rieg, Carolin'}, {'key': 'creator', 'value': 'Rieg, Carolin'}, {'key': 'date', 'value': '2021-04-09T00:00:00'}, {'key': 'identifier', 'value': 'https://doi.org/10.18419/darus-1326'}, {'key': 'metadata_modified', 'value': '2022-11-29T01:00:03'}, {'key': 'set_spec', 'value': 'all'}, {'key': 'harvest_object_id', 'value': '9f715c84-cc79-4b30-b503-e117948cec35'}, {'key': 'harvest_source_id', 'value': '8ba5ef26-d024-46cd-8099-94f1e74e7a36'}, {'key': 'harvest_source_title', 'value': 'Darus Test Harvest'}], 'resources': [{'cache_last_updated': None, 'cache_url': None, 'created': '2023-05-08T19:12:26.492289', 'format': 'HTML', 'hash': '', 'id': '4eb0ca7a-7d90-4a29-8c98-34f5c415921a', 'last_modified': None, 'metadata_modified': '2023-05-08T19:12:26.484859', 'mimetype': None, 'mimetype_inner': None, 'name': 'Publication data for: "A Method for the Selective Quantification of Bronsted Acid Sites on External Surfaces and in Mesopores of Hierarchical Zeolites" - data from Dyballa group', 'package_id': 'doi-10-18419-darus-1326', 'position': 0, 'resource_type': 'HTML', 'size': None, 'state': 'active', 'url': 'https://doi.org/10.18419/darus-1326', 'url_type': None}], 'tags': [{'display_name': 'catalysis', 'id': '109d3c51-8485-4605-ad00-c576d7092a7a', 'name': 'catalysis', 'state': 'active', 'vocabulary_id': None}, {'display_name': 'chemistry', 'id': '20e4e978-2a22-4286-a18b-4ae22d1ffca1', 'name': 'chemistry', 'state': 'active', 'vocabulary_id': None}, {'display_name': 'porous-materials', 'id': '0c4f3d0a-29bf-4919-af13-93a7f219a947', 'name': 'porous-materials', 'state': 'active', 'vocabulary_id': None}], 'groups': [], 'relationships_as_subject': [], 'relationships_as_object': []}, {'author': 'Rieg, Carolin', 'author_email': None, 'creator_user_id': '1be646ae-ab26-47b8-8835-e4b27f11961e', 'id': 'doi-10-18419-darus-1253', 'isopen': False, 'license_id': '', 'license_title': '', 'maintainer': 'DaRUS', 'maintainer_email': None, 'metadata_created': '2023-05-08T19:12:19.026517', 'metadata_modified': '2023-05-08T19:12:19.026523', 'name': 'doi-10-18419-darus-1253', 'notes': '<p>Different phosphines (PR3, R= phenyl, 4-methoxyphenyl) are demonstrated to be useful probe molecules for the spatial location and quantification of noble metal (NM) atoms within mesoporous and microporous support materials, such as silica A200, mesoporous SBA-15, and different zeolites Y. For this purpose, the high NMR sensitivity of 31P nuclei (spin I = ½, abundance of 100%) and the characteristic chemical shifts of phosphine complexes formed with noble metals were utilized. A straightforward method of physically mixing the reduced noble metal-containing catalysts with the solid phosphine powders and heating under well-defined conditions is shown. Complexation of triphenylphosphine (PPh3) and tris(4-methoxyphenyl)phosphine, P(4-CH3O-C6H4)3, with Pt, Rh, Pd, and Ru on open surfaces and in mesopores leads to characteristic 31P MAS NMR signals at δ = 33 to 41 ppm. Because of the different molecular diameters of PPh3 (0.72 nm) and P(4-CH3O-C6H4)3 (0.97 nm), adsorption of these two probe molecules allows for distinguishing between noble metal atoms located at the outer surface of zeolite particles and those in secondary mesopores and in supercages of zeolites Y. For the first time this method enables the characterization of noble metals directly using probe molecules and 31P MAS NMR spectroscopy.</p>\n\n<p>The uploaded data are sorted by the method of measurement, ICP-OES (inductively coupled plasma optical emission spectrometry), Physisorption (BET), Chemisorption and NMR. NMR files are uploaded as jcampdx data. Also, SEM (scanning electron microscopy) and TEM (transmission electron microscopy) images are uploaded. For the NMR data, the name of the corresponding figure is given, the figures SX can be found in the supporting information. The additional information "parent" signifies that the materials are not modified by noble metals.</p>', 'num_resources': 1, 'num_tags': 4, 'organization': {'id': '9a7d2a53-21f6-412a-afb9-a15122df0640', 'name': 'darus', 'title': 'DaRUS', 'type': 'repository', 'description': 'Chemistry collection from DaRUS, the data repository of the University of Stuttgart.', 'image_url': 'logoDarusKreis.png', 'created': '2023-05-03T09:01:04.791551', 'is_organization': True, 'approval_status': 'approved', 'state': 'active'}, 'owner_org': '9a7d2a53-21f6-412a-afb9-a15122df0640', 'private': False, 'related_molecule': [], 'state': 'active', 'title': 'Publication data for: "Noble metal location in porous supports determined by reaction with phosphines - data from Dyballa group"', 'type': 'dataset', 'extras': [{'key': 'contributor', 'value': 'Rieg, Carolin'}, {'key': 'creator', 'value': 'Rieg, Carolin'}, {'key': 'date', 'value': '2021-03-12T00:00:00'}, {'key': 'identifier', 'value': 'https://doi.org/10.18419/darus-1253'}, {'key': 'metadata_modified', 'value': '2022-11-29T01:00:03'}, {'key': 'set_spec', 'value': 'all'}, {'key': 'harvest_object_id', 'value': '0f9e4cd6-a23c-4043-85cb-d8a8a289b637'}, {'key': 'harvest_source_id', 'value': '8ba5ef26-d024-46cd-8099-94f1e74e7a36'}, {'key': 'harvest_source_title', 'value': 'Darus Test Harvest'}], 'resources': [{'cache_last_updated': None, 'cache_url': None, 'created': '2023-05-08T19:12:19.028188', 'format': 'HTML', 'hash': '', 'id': '4d21ede4-198a-4e74-a1e1-a11eda4e65a9', 'last_modified': None, 'metadata_modified': '2023-05-08T19:12:19.013824', 'mimetype': None, 'mimetype_inner': None, 'name': 'Publication data for: "Noble metal location in porous supports determined by reaction with phosphines - data from Dyballa group"', 'package_id': 'doi-10-18419-darus-1253', 'position': 0, 'resource_type': 'HTML', 'size': None, 'state': 'active', 'url': 'https://doi.org/10.18419/darus-1253', 'url_type': None}], 'tags': [{'display_name': 'chemistry', 'id': '20e4e978-2a22-4286-a18b-4ae22d1ffca1', 'name': 'chemistry', 'state': 'active', 'vocabulary_id': None}, {'display_name': 'confinement', 'id': '6cb7505c-f92e-435f-a1dc-e7542d4a061a', 'name': 'confinement', 'state': 'active', 'vocabulary_id': None}, {'display_name': 'experimental-data-solid-state-nmr', 'id': '5bff640b-0f0d-40a5-9d6e-91f8b6ac4eac', 'name': 'experimental-data-solid-state-nmr', 'state': 'active', 'vocabulary_id': None}, {'display_name': 'heterogeneous-catalysis', 'id': '86b5272a-37ca-43c8-b338-18e1995d1ff5', 'name': 'heterogeneous-catalysis', 'state': 'active', 'vocabulary_id': None}], 'groups': [], 'relationships_as_subject': [], 'relationships_as_object': []}, {'author': 'Jeltsch, Albert, Bashtrykov, Pavel, Bröhm, Alexander, Dukatz, Michael, Adam, Sabrina', 'author_email': None, 'creator_user_id': '1be646ae-ab26-47b8-8835-e4b27f11961e', 'id': 'doi-10-18419-darus-1252', 'isopen': False, 'language': 'English', 'license_id': '', 'license_title': '', 'maintainer': 'DaRUS', 'maintainer_email': None, 'metadata_created': '2023-05-08T19:12:18.866702', 'metadata_modified': '2023-05-08T19:12:18.866707', 'name': 'doi-10-18419-darus-1252', 'notes': '<p>Methylation experiments:<br> \nFor the competitive nucleosome methylation experiments, 0.6 pmol of each nucleosome variant were digested with MluI (NEB) for 60 min at 37°C in 10 µL NEB Cutsmart buffer (50 mM KOAc/20 mM Tris-acetate pH 7.9, 10 mM Magnesium Acetate, 100 µg/mL BSA) to remove residual unbound DNA. Afterwards, DNMT3A2 or DNMT3AC was added to the mixture to a final concentration ranging from 0.5 µM to 3 µM and in 80 µL NEB Cutsmart buffer supplemented with 10 mM EDTA and 25 µM AdoMet (Perkin Elmer). The methylation reaction was allowed to proceed for 2 h at 37°C. To stop the reaction and remove all nucleosome-bound proteins, proteinase K was added to the reaction and the sample was incubated for further 60 min at 37°C. The resulting unbound DNA was purified from the reaction mixture using the Nucleospin Gel and PCR cleanup kit (Macherey-Nagel). Bisulfite conversion of the methylated DNA was performed using the EZ DNA Methylation-Lightning kit (Zymo Research). Methylation of free DNA was conducted the same way using 15 µM DNA.</p>\n\n<p>Library preparation and sequencing analysis: <br>\nSample-specific barcodes and indices were added to the DNA by PCR amplification in a two-step PCR process. Briefly, in the first PCR, barcoded primers were used to amplify the bisulfite converted nucleosome DNA using the HotStartTaq Polymerase (Qiagen) and the resulting 321 bp fragment was purified using the Nucleospin Gel and PCR cleanup kit (Macherey-Nagel). In the second PCR step, adaptors and indices required for sequencing were added by amplification with the respective primers and the Phusion polymerase (ThermoFisher). The final 390-bp product was purified and used for Illumina paired end 2x250 bp sequencing. Datasets were analyzed using a local instance of the Galaxy bioinformatics server. Sequence reads were trimmed with the Trim Galore! Tool (developed by Felix Krueger at the Babraham Institute) and subsequently paired using PEAR. 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