cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17044/scilifelab.12213434.v1
title: Data from: A systems biology approach identifies B cell maturation antigen (BCMA) as biomarker reflecting oral vaccine induced IgA antibody responses in humans

description: In this study, RNA-Seq was performed on peripheral blood mononuclear cells (PBMCs) isolated from six
volunteers of a oral cholera Dukoral<sup>®</sup> vaccine study performed
by Mottram et al., 2020.(10.1016/j.vaccine.2019.10.050). 

 

<br>The raw FASQ and indexed aligned BAM files described here were taken
from four strong and two non IgA antibody responders of
this Dukoral<sup>®</sup> vaccine study and are part of another study described
by Mottram et al (2021) (Frontiers in Immunology, accepted for publication). <br>

 

Total RNA-Seq on these PMBCs was performed by GeneCore SU, University of
Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
(http://www.cgg.gu.se/genecore-su), using the Illumina Nextseq 500 platform
(Illumina, San Diego, CA, USA). cDNA libraries were prepared from total RNA
samples (≤1500ng), using the TruSeq
Stranded Total RNA Sample Preparation Kit with Ribo-zero Gold (Illumina Inc).
Each library was paired-end sequenced (2×75 bp) using the Illumina Nextseq500
Kit High Output V2.<br>

 

All sequencing
reads were analysed for quality control using the prinseq/0.20.3. Quality
filtered reads were aligned to the Ensembl human reference genome GRCh38.90
using star/2.5.2b. Read counts mapped towards annotated features were
calculated using the HTSeq-count/0.6.1p1 tool. Statistical analysis was
performed using DESeq2_1.14.1 within R/3.3 software, applying a
significance threshold padj &lt; 0.05. <br>The oral cholera<b> </b>Dukoral<sup>®</sup> vaccine study was performed in accordance with the declaration of Helsinki and Good Clinical practice guidelines. Dukoral<sup>®</sup> vaccinated volunteers provided their written informed consent to participate in these studies, including the RNA-seq of their PBMCs. Consequently, the raw RNA datasets are not publicly available. However, controlled access to these FASQ and BAM files can be made available after applying for access and agreeing to terms and conditions before use.<br><br>

 

<br><br>
DOI: 10.6084/m9.figshare.28212008.v1
title: Source data file-Virulence-253035411.xlsx

description: Supplementary Information for the submission(Virulence-253035411) to the Journal “Virulence”
DOI: 10.7483/opendata.cms.gd10.wa8i
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH100_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.15468/dl.32pybd
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hylis slipinskii Burakowski & Buchholz, 1991",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071180-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7483/opendata.cms.cfkz.nkot
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH100_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.12401906
title: SMCT-FCS data from DNA surface exploration and operator bypassing during target search

description: Single-molecule confocal laser tracking combined with fluorescence correlation spectroscopy dataset of lac repressor molecules sliding on flow-stretched DNA, as in Marklund et al., Nature, 2020.
DOI: 10.17044/scilifelab.12401906.v2
title: SMCT-FCS data from DNA surface exploration and operator bypassing during target search

description: Single-molecule confocal laser tracking combined with fluorescence correlation spectroscopy dataset of lac repressor molecules sliding on flow-stretched DNA, as in Marklund et al., Nature, 2020.
DOI: 10.7483/opendata.cms.zjxv.kcah
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH125_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.12401906.v1
title: raw_data_SMCT_FCS.tar.gz

description: Single-molecule confocal laser tracking combined with fluorescence correlation spectroscopy dataset of lac repressor molecules sliding on flow-stretched DNA, as in Marklund et al., Nature, 2020.
DOI: 10.7483/opendata.cms.rzvm.sv2b
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH125_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.12662153
title: Improved computational analysis of ribosome dynamics from 5’P degradome data using fivepeseq

description: Supplementary information for manuscript: "Improved computational analysis of ribosome dynamics from 5’P degradome data using fivepeseq" from Lilit Nersisyan, Maria Ropat and Vicent Pelechano (2020)<br>Dataset updated to fivepseq version1.0b6<br><br>5'P mRNA degradome datasets analyzed with fivepseq. (http://pelechanolab.com/software/fivepseq/). Raw <i>Saccharomyces cerevisiae</i> data is available from GEO under accession code GSE91064 and for <i>Arabidopsis thaliana</i> under accessions GSE72505 and GSE77549. <br>
DOI: 10.17044/scilifelab.12662153.v2
title: Improved computational analysis of ribosome dynamics from 5’P degradome data using fivepeseq

description: Supplementary information for manuscript: "Improved computational analysis of ribosome dynamics from 5’P degradome data using fivepeseq" from Lilit Nersisyan, Maria Ropat and Vicent Pelechano (2020)<br>Dataset updated to fivepseq version1.0b6<br><br>5'P mRNA degradome datasets analyzed with fivepseq. (http://pelechanolab.com/software/fivepseq/). Raw <i>Saccharomyces cerevisiae</i> data is available from GEO under accession code GSE91064 and for <i>Arabidopsis thaliana</i> under accessions GSE72505 and GSE77549. <br>
DOI: 10.17044/scilifelab.12662153.v1
title: Improved computational analysis of ribosome dynamics from 5’P degradome data using fivepeseq

description: Supplementary information for manuscript: "Improved computational analysis of ribosome dynamics from 5’P degradome data using fivepeseq" from Lilit Nersisyan, Maria Ropat and Vicent Pelechano (2020)5'P mRNA degradome datasets analyzed with fivepseq. (http://pelechanolab.com/software/fivepseq/). Raw <i>Saccharomyces cerevisiae</i> data is available from GEO under accession code GSE91064 and for <i>Arabidopsis thaliana</i> under accessions GSE72505 and GSE77549. <br>
DOI: 10.7483/opendata.cms.qxh0.kr12
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH150_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.48579/pro/cgt7d7
title: Collection of rasters and social ecological indicators for Zone Atelier Pyrénées Garonne

description: Open, world wide rasters (biogeoregions, land surface temperature, normalised difference vegetation index, population density and land cover) are cropped with respect to the polygon of the Zone Atelier Environmental Urban so as to compute indicators. This dataset contains the shapefile, rasters for variables BIOG (biogeoregion), LSTD (land surface temperature day), LSTN (land surface temperature night), NDVI (normalized difference vegetation index), GPW4 (population density), and LC (land cover) cropped with respect to the shapefile, and social ecological indicators for these variables computed as averages or quantiles.
DOI: 10.7483/opendata.cms.6nex.i60a
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH150_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17632/n3gcx2ds6t.1
title: Candy Dataset - Faculty of Engineering - University of Porto - Department of Mechanical Engineering

description: This repository presents the "Candy Dataset".

The repository contains a single file that comprises an authentic dataset. For user convenience, it is available for download in various formats, including YOLOV11, YOLOV10, YOLOV9, YOLOv8, YOLOV6,YOLOv5, YOLOv7, MT-YOLOv6, COCO JSON, YOLO Darknet, Pascal VOC XML, TFRecord, CreateML JSON, and Other Formats.

Ultimately, this dataset is available for download in zip format. Also includes the kinematic and dynamic parameters of the Collaborative Robot.

Any publications utilizing the 'Candy Dataset' must properly cite the following paper:
Santos, A.A., Schreurs, C., da Silva, A.F. et al. Integration of Artificial Vision and Image Processing into a Pick and Place Collaborative Robotic System. J Intell Robot Syst 110, 159 (2024). https://doi.org/10.1007/s10846-024-02195-z
DOI: 10.7483/opendata.cms.h77p.s8zm
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH175_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.7483/opendata.cms.f07o.e98e
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH175_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.7483/opendata.cms.l7az.na24
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH200_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.13089023
title: Thermal Proteome Profiling dataset from Hazara virus infected SW13 cells treated with DMSO or antiviral inhibitor 20 µM TH6744.

description: <b>Article: </b>S3 Dataset from a publication "Tampere, M.; Pettke, A.; Salata, C.; Wallner, O.; Koolmeister, T.; Cazares-Körner, A.; Visnes, T.; Hesselman, M.C.; Kunold, E.; Wiita, E.; Kalderén, C.; Lightowler, M.; Jemth, A.-S.; Lehtiö, J.; Rosenquist, Å.; Warpman-Berglund, U.; Helleday, T.; Mirazimi, A.; Jafari, R.; Puumalainen, M.-R. Novel Broad-Spectrum Antiviral Inhibitors Targeting Host Factors Essential for Replication of Pathogenic RNA Viruses. <em>Viruses</em> 2020, <em>12</em>, 1423." <br><b>Abstract: </b>Recent RNA virus outbreaks such as Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Ebola virus (EBOV) have caused worldwide health emergencies highlighting the urgent need for new antiviral strategies. Targeting host cell pathways supporting viral replication is an attractive approach for development of antiviral compounds, especially with new, unexplored viruses where knowledge of virus biology is limited. Here, we present a strategy to identify host-targeted small molecule inhibitors using an image-based phenotypic antiviral screening assay followed by extensive target identification efforts revealing altered cellular pathways upon antiviral compound treatment. The newly discovered antiviral compounds showed broad-range antiviral activity against pathogenic RNA viruses such as SARS-CoV-2, EBOV and Crimean-Congo hemorrhagic fever virus (CCHFV). Target identification of the antiviral compounds by thermal protein profiling revealed major effects on proteostasis pathways and disturbance in interactions between cellular HSP70 complex and viral proteins, illustrating the supportive role of HSP70 on many RNA viruses across virus families. Collectively, this strategy identifies new small molecule inhibitors with broad antiviral activity against pathogenic RNA viruses, but also uncovers novel virus biology urgently needed for design of new antiviral therapies.<br><b>Data processing: </b>Current processed dataset in Excel format originates from Thermal Proteome Profiling (TPP-TR) performed on Hazara virus infected cells treated with DMSO or antiviral inhibitor 20 µM TH6744. The raw MS/MS data was searched against the UniProt Homo Sapiens database (containing canonical and isoforms_42144 entries downloaded on March 21st 2016) using Mascot. Summarized are a list of proteins identified in each replicate and experimental condition. <b><br></b><b>Data authors: </b>Data was generated by Marianna Tampere, Rozbeh Jafari and Marjo-Riitta Puumalainen in March 2016. <br>
DOI: 10.17044/scilifelab.13089023.v1
title: Thermal Proteome Profiling dataset from Hazara virus infected SW13 cells treated with DMSO or antiviral inhibitor 20 µM TH6744.

description: <b>Article: </b>S3 Dataset from a publication "Tampere, M.; Pettke, A.; Salata, C.; Wallner, O.; Koolmeister, T.; Cazares-Körner, A.; Visnes, T.; Hesselman, M.C.; Kunold, E.; Wiita, E.; Kalderén, C.; Lightowler, M.; Jemth, A.-S.; Lehtiö, J.; Rosenquist, Å.; Warpman-Berglund, U.; Helleday, T.; Mirazimi, A.; Jafari, R.; Puumalainen, M.-R. Novel Broad-Spectrum Antiviral Inhibitors Targeting Host Factors Essential for Replication of Pathogenic RNA Viruses. <em>Viruses</em> 2020, <em>12</em>, 1423." <br><b>Abstract: </b>Recent RNA virus outbreaks such as Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Ebola virus (EBOV) have caused worldwide health emergencies highlighting the urgent need for new antiviral strategies. Targeting host cell pathways supporting viral replication is an attractive approach for development of antiviral compounds, especially with new, unexplored viruses where knowledge of virus biology is limited. Here, we present a strategy to identify host-targeted small molecule inhibitors using an image-based phenotypic antiviral screening assay followed by extensive target identification efforts revealing altered cellular pathways upon antiviral compound treatment. The newly discovered antiviral compounds showed broad-range antiviral activity against pathogenic RNA viruses such as SARS-CoV-2, EBOV and Crimean-Congo hemorrhagic fever virus (CCHFV). Target identification of the antiviral compounds by thermal protein profiling revealed major effects on proteostasis pathways and disturbance in interactions between cellular HSP70 complex and viral proteins, illustrating the supportive role of HSP70 on many RNA viruses across virus families. Collectively, this strategy identifies new small molecule inhibitors with broad antiviral activity against pathogenic RNA viruses, but also uncovers novel virus biology urgently needed for design of new antiviral therapies.<br><b>Data processing: </b>Current processed dataset in Excel format originates from Thermal Proteome Profiling (TPP-TR) performed on Hazara virus infected cells treated with DMSO or antiviral inhibitor 20 µM TH6744. The raw MS/MS data was searched against the UniProt Homo Sapiens database (containing canonical and isoforms_42144 entries downloaded on March 21st 2016) using Mascot. Summarized are a list of proteins identified in each replicate and experimental condition. <b><br></b><b>Data authors: </b>Data was generated by Marianna Tampere, Rozbeh Jafari and Marjo-Riitta Puumalainen in March 2016. <br>
DOI: 10.7483/opendata.cms.01xp.dl4e
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH200_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.7483/opendata.cms.v5ei.p02l
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH250_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.7483/opendata.cms.691k.swhb
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH250_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.13181273.v1
title: Consiglio et al 2020 Cell The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19

description: Publication: "The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19". <br>Plasma protein profiling was performed at SciLifeLab's Translational Plasma Profiling Facility. The datasets, metadata and supplementary tables here include multiple omics data from plasma protein expression (Olink - NPX values), FACS and Autoantibodies. See README file for description of files attached.<br><br> Publication summary: "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is typically very mild and often asymptomatic in children. A complication is the rare multisystem inflammatory syndrome in children (MISC) associated with COVID-19, presenting 4–6 weeks after infection as high fever, organ dysfunction, and strongly elevated markers of inflammation. The pathogenesis is unclear but has overlapping features with Kawasaki disease suggestive of vasculitis and a likely autoimmune etiology. We apply systems-level analyses of blood immune cells, cytokines, and autoantibodies in healthy children, children with Kawasaki disease enrolled prior to COVID-19, children infected with SARS-CoV-2, and children presenting with MIS-C. We find that the inflammatory response in MIS-C differs from the cytokine storm of severe acute COVID-19, shares several features with Kawasaki disease, but also differs from this condition with respect to T cell subsets, interleukin (IL)-17A, and biomarkers associated with arterial damage. Finally, autoantibody profiling suggests multiple autoantibodies that could be involved in the pathogenesis of MIS-C."
DOI: 10.7483/opendata.cms.1syl.o2pt
title: /TprimeBToTH_TLep_Hbb_LH_MT2400_MH25_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.13181273
title: Consiglio et al 2020 Cell The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19

description: Publication: "The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19". <br>Plasma protein profiling was performed at SciLifeLab's Translational Plasma Profiling Facility. The datasets, metadata and supplementary tables here include multiple omics data from plasma protein expression (Olink - NPX values), FACS and Autoantibodies. See README file for description of files attached.<br><br> Publication summary: "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is typically very mild and often asymptomatic in children. A complication is the rare multisystem inflammatory syndrome in children (MISC) associated with COVID-19, presenting 4–6 weeks after infection as high fever, organ dysfunction, and strongly elevated markers of inflammation. The pathogenesis is unclear but has overlapping features with Kawasaki disease suggestive of vasculitis and a likely autoimmune etiology. We apply systems-level analyses of blood immune cells, cytokines, and autoantibodies in healthy children, children with Kawasaki disease enrolled prior to COVID-19, children infected with SARS-CoV-2, and children presenting with MIS-C. We find that the inflammatory response in MIS-C differs from the cytokine storm of severe acute COVID-19, shares several features with Kawasaki disease, but also differs from this condition with respect to T cell subsets, interleukin (IL)-17A, and biomarkers associated with arterial damage. Finally, autoantibody profiling suggests multiple autoantibodies that could be involved in the pathogenesis of MIS-C."
DOI: 10.17044/scilifelab.13229168
title: 5PSeq analysis conecting translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae

description: Supplementary information for the manuscript: A functional connection between translation elongation and protein folding at the ribosome exit tunnel in <i>Saccharomyces cerevisiae. </i>Olga Rodríguez-Galán, Juan J García-Gómez, Iván V Rosado, Wu Wei, Alfonso Méndez-Godoy, Benjamin Pillet, Alisa Alekseenko, Lars M Steinmetz, Vicent Pelechano, Dieter Kressler, Jesús de la Cruz, Nucleic Acids Research, , gkaa1200, https://doi.org/10.1093/nar/gkaa1200<br>Here we provide browsable metagene analysis for 5´P mRNA degradation profiles.Raw and processed sequencing data are deposited at Gene Expression Omnibus (GEO) with accession numbers GSE114899. Data was analyzed using <i>fivepseq</i> pipeline http://pelechanolab.com/software/fivepseq/<br><b>Related manuscript abstract:</b><br>Proteostasis needs to be tightly controlled to meet the cellular demand for correctly de novo folded proteins and to avoid protein aggregation. While a coupling between translation rate and co-translational folding, likely involving an interplay between the ribosome and its associated chaperones, clearly appears to exist, the underlying mechanisms and the contribution of ribosomal proteins remain to be explored. The ribosomal protein uL3 contains a long internal loop whose tip region is in close proximity to the ribosomal peptidyl transferase center. Intriguingly, the <i>rpl3</i>[W255C] allele, in which the residue making the closest contact to this catalytic site is mutated, affects diverse aspects of ribosome biogenesis and function. Here, we have uncovered, by performing a synthetic lethal screen with this allele, an unexpected link between translation and the folding of nascent proteins by the ribosome-associated Ssb-RAC chaperone system. Our results reveal that uL3 and Ssb-RAC cooperate to prevent 80S ribosomes from piling up within the 5’ region of mRNAs early on during translation elongation. Together, our study provides compelling in vivo evidence for a functional connection between peptide bond formation at the peptidyl transferase center and chaperone-assisted de novo folding of nascent polypeptides at the solvent-side of the peptide exit tunnel.<br><b>Raw data:</b>Raw and processed sequencing data are deposited at Gene Expression Omnibus (GEO) with accession number GSE114899 and GSE151632<br><br>
DOI: 10.17044/scilifelab.13229168.v1
title: 5PSeq analysis conecting translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae

description: Supplementary information for the manuscript: A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae. Rodríguez-Galán, Juan J. García-Gómez, Iván V. Rosado, Wu Wei, Alfonso Méndez-Godoy, Benjamin Pillet, Alisa Alekseenko, Lars M. Steinmetz, Vicent Pelechano, Dieter Kressler and Jesús de la Cruz.Here we provide browsable metagene analysis for 5´P mRNA degradation profiles.Raw and processed sequencing data are deposited at Gene Expression Omnibus (GEO) with accession numbers GSE114899. Data was analyzed using <i>fivepseq</i> pipeline http://pelechanolab.com/software/fivepseq/<br>Manuscript abstract:<br>Proteostasis needs to be tightly controlled to meet the cellular demand for correctly de novo folded proteins and to avoid protein aggregation. While a coupling between translation rate and co-translational folding, likely involving an interplay between the ribosome and its associated chaperones, clearly appears to exist, the underlying mechanisms and the contribution of ribosomal proteins remain to be explored. The ribosomal protein uL3 contains a long internal loop whose tip region is in close proximity to the ribosomal peptidyl transferase center. Intriguingly, the <i>rpl3</i>[W255C] allele, in which the residue making the closest contact to this catalytic site is mutated, affects diverse aspects of ribosome biogenesis and function. Here, we have uncovered, by performing a synthetic lethal screen with this allele, an unexpected link between translation and the folding of nascent proteins by the ribosome-associated Ssb-RAC chaperone system. Our results reveal that uL3 and Ssb-RAC cooperate to prevent 80S ribosomes from piling up within the 5’ region of mRNAs early on during translation elongation. Together, our study provides compelling in vivo evidence for a functional connection between peptide bond formation at the peptidyl transferase center and chaperone-assisted de novo folding of nascent polypeptides at the solvent-side of the peptide exit tunnel.<br><br>