cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22710250
title: ExtData_Figure_1_images_for_paper

description: <em>B) Protein lysates of Xrn1 knock out A549 cells infected with WT PR8 or PR8-PA(∆X), or mock infected, were probed with antibodies against PR8 PA or b-tubulin as a loading control. Images are representative of 2 experiments. </em> <em>(C) Protein lysates of WT or Xrn1 knock out (ko) A549 cells were probed with antibodies against Xrn1 or b-tubulin as a loading control to check for loss of Xrn1. Images are representative of 2 experiments. </em> <em>R# --&gt; replicate number; LG### --&gt; experiment number. Additional replicates are found in ExtData_Figure_1_replicates dataset.</em> <em>.sgd files are original source files acquired with Syngene Imager.</em>
DOI: 10.6084/m9.figshare.22710619
title: ExtData_Figure_9_images_for_paper

description: <em>(A-B) Xrn1 knock out A549 cells were infected with WT PR8 or PR8-PA(∆X) (A), or WT H1N1pdm09 or H1N1pdm09-PA(∆X) (B), or mock infected. RNA was extracted to run 5’ RACE using primers ~150-200 nt downstream of GCUG sites that are predicted to be in a hairpin loop in the indicated viral mRNAs. Gel images used in paper are representative of 3 experiments. </em> <em>R# --&gt; replicate number; LG### --&gt; experiment number</em> <em>.sgd files are the original source files acquired with the Syngene imager</em>
DOI: 10.6084/m9.figshare.22696663
title: Figure_3_images_used_in_paper

description: <em>(F-G) HEK293T ishXrn1cells were treated with doxycycline for 3-4 days to induce knock down of Xrn1, then transfected with luciferase reporters containing 99 bp insertions from </em>STOML2 <em>and </em>YKT6<em> with or without a GCTG to TAGC mutation at the cut site (F), a repeat of the luciferase cut site (G), or the GCTG tetramer alone (G), together with PR8 PA-X or an empty vector. RNA was extracted to run 5’ RACE. DNA bands were purified and sequenced to confirm their identities. Gel images are representative of 3 experiments. Images for additional replicates are in folder Figure_3_replicates.</em> <em>R## --&gt; replicate number; LG## --&gt; experiment number.</em> <em>sgd files --&gt; original source files obtained with Syngene imager</em>
DOI: 10.6084/m9.figshare.22705399
title: Figure_4_images_used_for_paper

description: <em>(B, F, G) HEK293T ishXrn1cells were treated with doxycycline for 3-4 days to induce knock down of Xrn1, then transfected with luciferase reporters containing insertions of the indicated lengths from the </em>YKT6<em> or </em>STOML2<em> genes (B). In F and G, constructs also carry mutations that disrupt the hairpin structure and restore with a different sequence. PR8 PA-X or an empty vector were also co-transfected. RNA was extracted to run 5’ RACE. DNA bands were purified and sequenced to confirm their identities. Gel images representative of 3 experiments. Additional replicates are located in Figure_4_replicates dataset.</em> <em>R# --&gt; replicate number; AI#/LG### --&gt; experiment number.</em> <em>.sgd are the original source files acquired with the Syngene Imager.</em>
DOI: 10.6084/m9.figshare.22705399.v1
title: Figure_4_images_used_for_paper

description: <em>(B, F, G) HEK293T ishXrn1cells were treated with doxycycline for 3-4 days to induce knock down of Xrn1, then transfected with luciferase reporters containing insertions of the indicated lengths from the </em>YKT6<em> or </em>STOML2<em> genes (B). In F and G, constructs also carry mutations that disrupt the hairpin structure and restore with a different sequence. PR8 PA-X or an empty vector were also co-transfected. RNA was extracted to run 5’ RACE. DNA bands were purified and sequenced to confirm their identities. Gel images representative of 3 experiments. Additional replicates are located in Figure_4_replicates dataset.</em> <em>R# --&gt; replicate number; AI#/LG### --&gt; experiment number.</em> <em>.sgd are the original source files acquired with the Syngene Imager.</em>
DOI: 10.6084/m9.figshare.22705423
title: Figure_4_replicates

description: <em>(B, F, G) HEK293T ishXrn1cells were treated with doxycycline for 3-4 days to induce knock down of Xrn1, then transfected with luciferase reporters containing insertions of the indicated lengths from the </em>YKT6<em> or </em>STOML2<em> genes (B). In F and G, constructs also carry mutations that disrupt the hairpin structure and restore with a different sequence. PR8 PA-X or an empty vector were also co-transfected. RNA was extracted to run 5’ RACE. DNA bands were purified and sequenced to confirm their identities.</em> <em>R# --&gt; replicate number; AI#/LG### --&gt; experiment number.</em> <em>.sgd are the original source files acquired with the Syngene Imager.</em>
DOI: 10.6084/m9.figshare.22705720
title: Figure_5_images_for_paper

description: <em>(G-I) Viral RNA was extracted from viral stocks (G), Xrn1 knock out A549 cells 16 hours post-infection (H), or 48-hour supernatants from infected MDCK cells (H). Viruses analyzed: </em> <em>WT PR8 and PR8-PA(∆X) strains with no insert, or PR8 with WT or mutant </em>STOML2<em> sequences inserted in the WT PR8 or PR8-PA(∆X) background. Mutant </em>STOML2<em> sequences contain the GCUG to UAGC mutation preventing PA-X cleavage. Viral RNA was reverse-transcribed and PCR-amplified using primers shown as black arrows in F-G to determine whether the </em>STOML2<em> sequences were retained. Gel images representative of 3 experiments with separate virus rescues. Additional replicates can be found in Figure_5_replicates dataset.</em> <em>R# --&gt; replicate number; LG### --&gt; experiment number</em> <em>.sgd are the original source files obtained with the Syngene Imager</em>
DOI: 10.6084/m9.figshare.22705726
title: Figure_5_replicates

description: <em>(G-I) Viral RNA was extracted from viral stocks (G), Xrn1 knock out A549 cells 16 hours post-infection (H), or 48-hour supernatants from infected MDCK cells (H). Viruses analyzed: </em> <em>WT PR8 and PR8-PA(∆X) strains with no insert, or PR8 with WT or mutant </em>STOML2<em> sequences inserted in the WT PR8 or PR8-PA(∆X) background. Mutant </em>STOML2<em> sequences contain the GCUG to UAGC mutation preventing PA-X cleavage. Viral RNA was reverse-transcribed and PCR-amplified using primers shown as black arrows in F-G to determine whether the </em>STOML2<em> sequences were retained.</em> <em>R# --&gt; replicate number; LG### --&gt; experiment number</em> <em>.sgd are the original source files obtained with the Syngene Imager</em>
DOI: 10.6084/m9.figshare.22693261.v1
title: Figure_1_qPCR

description: <em>(B-C) Wild-type (B) or Xrn1 knock out (B-C) A549 cells were either mock infected or infected with WT PR8 or PR8-PA(∆X) for 16 hours before RNA extraction. mRNA levels of influenza A virus HA and human G6PD, a PA-X target, were quantified by qRT-PCR and normalized by 18S rRNA levels. n = 3 independent experiments. R# --&gt; replicate number; LG### --&gt; experiment number/</em>
DOI: 10.6084/m9.figshare.22696411
title: Figure_2_images_used_in_paper

description: <em>(B) Xrn1 knock out A549 cells were infected with WT or PR8-PA(∆X), or mock infected for 16 hours before RNA extraction. 5’RACE was then performed using primers specific for </em>STOML2<em> or </em>YKT6<em>, ~250-300 nucleotides (nt) downstream of the predicted cut sites. The PCR products were run on an agarose gel. (D-F) HEK293T ishXrn1 cells were treated with doxycycline for 3-4 days to induce knock down of Xrn1, then transfected with luciferase reporters carrying a duplicate cut site from the reporter itself, or additional sequences from the </em>STOML2 and YKT6 <em>genes (99 bp around putative cut sites), and where indicated, with PA-X from the PR8 (D-F), H1N1pdm09 or Perth influenza strains (F). RNA was extracted to run 5’ RACE (D, F) or northern blotting (E).For all DNA gels, the DNA bands were purified and sequenced to confirm their identities. R## --&gt; replicate number; LG##/MMG### --&gt; experiment number. Additional replicates are found in Figure_2_replicates folder.</em> <em>sgd files --&gt; original source files obtained with Syngene imager</em>
DOI: 10.6084/m9.figshare.22696456
title: Figure_2_replicates

description: <em>(B) Xrn1 knock out A549 cells were infected with WT or PR8-PA(∆X), or mock infected for 16 hours before RNA extraction. 5’RACE was then performed using primers specific for </em>STOML2<em> or </em>YKT6<em>, ~250-300 nucleotides (nt) downstream of the predicted cut sites. The PCR products were run on an agarose gel. (D-F) HEK293T ishXrn1 cells were treated with doxycycline for 3-4 days to induce knock down of Xrn1, then transfected with luciferase reporters carrying a duplicate cut site from the reporter itself, or additional sequences from the </em>STOML2 and YKT6 <em>genes (99 bp around putative cut sites), and where indicated, with PA-X from the PR8 (D-F), H1N1pdm09 or Perth influenza strains (F). RNA was extracted to run 5’ RACE (D, F) or northern blotting (E).For all DNA gels, the DNA bands were purified and sequenced to confirm their identities. R## --&gt; replicate number; LG###/MMG#### --&gt; experiment number. sgd files --&gt; original source files obtained with Syngene imager</em>
DOI: 10.6084/m9.figshare.22696663.v1
title: Figure_3_images_used_in_paper

description: <em>(F-G) HEK293T ishXrn1cells were treated with doxycycline for 3-4 days to induce knock down of Xrn1, then transfected with luciferase reporters containing 99 bp insertions from </em>STOML2 <em>and </em>YKT6<em> with or without a GCTG to TAGC mutation at the cut site (F), a repeat of the luciferase cut site (G), or the GCTG tetramer alone (G), together with PR8 PA-X or an empty vector. RNA was extracted to run 5’ RACE. DNA bands were purified and sequenced to confirm their identities. Gel images are representative of 3 experiments. Images for additional replicates are in folder Figure_3_replicates.</em> <em>R## --&gt; replicate number; LG## --&gt; experiment number.</em> <em>sgd files --&gt; original source files obtained with Syngene imager</em>
DOI: 10.6084/m9.figshare.22696687
title: Figure_3_replicates

description: <em>(F-G) HEK293T ishXrn1cells were treated with doxycycline for 3-4 days to induce knock down of Xrn1, then transfected with luciferase reporters containing 99 bp insertions from </em>STOML2 <em>and </em>YKT6<em> with or without a GCTG to TAGC mutation at the cut site (F), a repeat of the luciferase cut site (G), or the GCTG tetramer alone (G), together with PR8 PA-X or an empty vector. RNA was extracted to run 5’ RACE. DNA bands were purified and sequenced to confirm their identities. Gel images are representative of 3 experiments.</em> <em>R## --&gt; replicate number; LG## --&gt; experiment number.</em> <em>sgd files --&gt; original source files obtained with Syngene imager</em>
DOI: 10.6084/m9.figshare.22693261
title: Figure_1_qPCR

description: <em>(B-C) Wild-type (B) or Xrn1 knock out (B-C) A549 cells were either mock infected or infected with WT PR8 or PR8-PA(∆X) for 16 hours before RNA extraction. mRNA levels of influenza A virus HA and human G6PD, a PA-X target, were quantified by qRT-PCR and normalized by 18S rRNA levels. n = 3 independent experiments. R# --&gt; replicate number; LG### --&gt; experiment number/</em>
DOI: 10.6084/m9.figshare.22696411.v1
title: Figure_2_images_used_in_paper

description: <em>(B) Xrn1 knock out A549 cells were infected with WT or PR8-PA(∆X), or mock infected for 16 hours before RNA extraction. 5’RACE was then performed using primers specific for </em>STOML2<em> or </em>YKT6<em>, ~250-300 nucleotides (nt) downstream of the predicted cut sites. The PCR products were run on an agarose gel. (D-F) HEK293T ishXrn1 cells were treated with doxycycline for 3-4 days to induce knock down of Xrn1, then transfected with luciferase reporters carrying a duplicate cut site from the reporter itself, or additional sequences from the </em>STOML2 and YKT6 <em>genes (99 bp around putative cut sites), and where indicated, with PA-X from the PR8 (D-F), H1N1pdm09 or Perth influenza strains (F). RNA was extracted to run 5’ RACE (D, F) or northern blotting (E).For all DNA gels, the DNA bands were purified and sequenced to confirm their identities. R## --&gt; replicate number; LG##/MMG### --&gt; experiment number. Additional replicates are found in Figure_2_replicates folder.</em> <em>sgd files --&gt; original source files obtained with Syngene imager</em>
DOI: 10.25919/0757-gx07
title: Parkes observations for project PX500 semester 2023APRS_01

description: This proposal relates to time purchased by the Chinese Academy of Sciences for Parkes follow-up confirmation and timing of FAST discoveries. As the observing time has been purchased this proposal (and the related PX501) does not require TAC grading. The primary reason for submitting a proposal is to ensure an outreach statement and that the proposal is entered into OPAL for the data archive to access. The Chinese team have two time requests. The time scheduled for the first, relating to this proposal, will be allocated in blocks of 24 hours and the data will become available in the data archive with an 18 month embargo period. The second type of time will be scheduled in shorter blocks and the data archived with a 10 year embargo.
DOI: 10.5281/zenodo.7430103
title: Tables for "Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas"

description: <strong>Table 1. CCF Specimen, Biological Structure, and Spatial Ontology. </strong>For each ontology, we provide all class names, property names, entity Internationalized Resource Identifier (IRI), definition when available, and entity type. <strong>Table 2. 3D Reference Objects. </strong>The 3rd HRA release features 53 <em>Spatial Entities</em> of type <em>Spatial Object Reference</em> that are linked to anatomical structures in the ASCT+B tables plus 43 <em>Spatial Entities</em> of type <em>Extraction Site</em>. For each entity, we provide the spatial entity<em> </em>name, 3D object file name, ID and version number, organ label, sex, and type. Note that a landmark is a <em>Spatial Entity</em> that has been tagged as an <em>Extraction Set</em> for a specific <em>Extraction Site</em>, see <strong>Table 3</strong>. <strong>Table 3. Registered Tissue Data. </strong>This table shows 364 <em>Extraction Site </em>entities that either represent the registration location for <em>Tissue Blocks</em> or <em>Registration Sites</em>. For each, we provide consortium name and entity ID, HuBMAP ID if available, and experimental data donor sex as well as HRA data such as organ name, sex, Uberon ID, and GLB file. The data comes from four consortia. HuBMAP data includes 306 tissue blocks, and many of these have derived tissue sections with one or more associated datasets. The 29 well-defined GTEx extraction set sites link to 5,397 datasets. The 26 SPARC blocks link to one paper while the three KPMP tissue blocks link to two data publications.
DOI: 10.5281/zenodo.7430104
title: Tables for "Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas"

description: <strong>Table 1. CCF Specimen, Biological Structure, and Spatial Ontology. </strong>For each ontology, we provide all class names, property names, entity Internationalized Resource Identifier (IRI), definition when available, and entity type. <strong>Table 2. 3D Reference Objects. </strong>The 3rd HRA release features 53 <em>Spatial Entities</em> of type <em>Spatial Object Reference</em> that are linked to anatomical structures in the ASCT+B tables plus 43 <em>Spatial Entities</em> of type <em>Extraction Site</em>. For each entity, we provide the spatial entity<em> </em>name, 3D object file name, ID and version number, organ label, sex, and type. Note that a landmark is a <em>Spatial Entity</em> that has been tagged as an <em>Extraction Set</em> for a specific <em>Extraction Site</em>, see <strong>Table 3</strong>. <strong>Table 3. Registered Tissue Data. </strong>This table shows 364 <em>Extraction Site </em>entities that either represent the registration location for <em>Tissue Blocks</em> or <em>Registration Sites</em>. For each, we provide consortium name and entity ID, HuBMAP ID if available, and experimental data donor sex as well as HRA data such as organ name, sex, Uberon ID, and GLB file. The data comes from four consortia. HuBMAP data includes 306 tissue blocks, and many of these have derived tissue sections with one or more associated datasets. The 29 well-defined GTEx extraction set sites link to 5,397 datasets. The 26 SPARC blocks link to one paper while the three KPMP tissue blocks link to two data publications.
DOI: 10.5281/zenodo.7884315
title: Generated Wikidata Subset for Taxons based on dump: GeneTaxon_wikidata-20190121-all

description: Source file: GeneTaxon_wikidata-20190121-all.ttl.gz ShEx: https://github.com/kg-subsetting/paper-wikidata-subsetting-2023/blob/master/flexibility-experiments/genes%2Btaxons/GeneTaxon.shex More information: https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation
description: {"references": ["https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation"]}
DOI: 10.5281/zenodo.7884316
title: Generated Wikidata Subset for Taxons based on dump: GeneTaxon_wikidata-20190121-all

description: Source file: GeneTaxon_wikidata-20190121-all.ttl.gz ShEx: https://github.com/kg-subsetting/paper-wikidata-subsetting-2023/blob/master/flexibility-experiments/genes%2Btaxons/GeneTaxon.shex More information: https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation
description: {"references": ["https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation"]}
DOI: 10.5281/zenodo.7884296
title: Generated Wikidata Subset for Taxons based on dump: GeneTaxon_wikidata-20180115-all

description: Source file: GeneTaxon_wikidata-20180115-all.ttl.gz ShEx: https://github.com/kg-subsetting/paper-wikidata-subsetting-2023/blob/master/flexibility-experiments/genes%2Btaxons/GeneTaxon.shex More information: https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation
description: {"references": ["https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation"]}
DOI: 10.5281/zenodo.7884297
title: Generated Wikidata Subset for Taxons based on dump: GeneTaxon_wikidata-20180115-all

description: Source file: GeneTaxon_wikidata-20180115-all.ttl.gz ShEx: https://github.com/kg-subsetting/paper-wikidata-subsetting-2023/blob/master/flexibility-experiments/genes%2Btaxons/GeneTaxon.shex More information: https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation
description: {"references": ["https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation"]}
DOI: 10.5281/zenodo.7884080
title: Generated Wikidata Subset for Taxons based on dump: 20160613-all

description: Source file: GeneTaxon_wikidata-20160613-all.ttl.gz ShEx: https://github.com/kg-subsetting/paper-wikidata-subsetting-2023/blob/master/flexibility-experiments/genes%2Btaxons/GeneTaxon.shex More information: https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation
description: {"references": ["https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation"]}
DOI: 10.5281/zenodo.7884081
title: Generated Wikidata Subset for Taxons based on dump: 20160613-all

description: Source file: GeneTaxon_wikidata-20160613-all.ttl.gz ShEx: https://github.com/kg-subsetting/paper-wikidata-subsetting-2023/blob/master/flexibility-experiments/genes%2Btaxons/GeneTaxon.shex More information: https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation
description: {"references": ["https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation"]}
DOI: 10.5281/zenodo.7884056
title: Generated Wikidata Subset for Taxons based on dump: wikidata-20150601-all

description: Source file: GeneTaxon_wikidata-20150601-all.ttl.gz ShEx: https://github.com/kg-subsetting/paper-wikidata-subsetting-2023/blob/master/flexibility-experiments/genes%2Btaxons/GeneTaxon.shex More information: https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation
description: {"references": ["https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation"]}
DOI: 10.5281/zenodo.7884057
title: Generated Wikidata Subset for Taxons based on dump: wikidata-20150601-all

description: Source file: GeneTaxon_wikidata-20150601-all.ttl.gz ShEx: https://github.com/kg-subsetting/paper-wikidata-subsetting-2023/blob/master/flexibility-experiments/genes%2Btaxons/GeneTaxon.shex More information: https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation
description: {"references": ["https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation"]}
DOI: 10.5281/zenodo.7872555
title: Generated Wikidata Subset for geneWiki based on dump: GeneWiki_wikidata-20170821-all

description: Source file: GeneWiki_wikidata-20170821-all.ttl.gz
DOI: 10.5281/zenodo.7872554
title: Generated Wikidata Subset for geneWiki based on dump: GeneWiki_wikidata-20170821-all

description: Source file: GeneWiki_wikidata-20170821-all.ttl.gz
DOI: 10.5281/zenodo.7884512
title: Machine learning meets pKa - Datasets

description: Datesets belonging to the publication: Baltruschat M and Czodrowski P. Machine learning meets pK<sub>a</sub> [version 2; peer review: 2 approved]. <em>F1000Research</em> 2020, <strong>9</strong>(Chem Inf Sci):113 (https://doi.org/10.12688/f1000research.22090.2) Corresponding GitHub repository: https://github.com/czodrowskilab/Machine-learning-meets-pKa
DOI: 10.5281/zenodo.7884511
title: Machine learning meets pKa - Datasets

description: Datesets belonging to the publication: Baltruschat M and Czodrowski P. Machine learning meets pK<sub>a</sub> [version 2; peer review: 2 approved]. <em>F1000Research</em> 2020, <strong>9</strong>(Chem Inf Sci):113 (https://doi.org/10.12688/f1000research.22090.2) Corresponding GitHub repository: https://github.com/czodrowskilab/Machine-learning-meets-pKa