cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17044/scilifelab.24999260.v1
title: Multiplexed Mapping of the Interactome of GPCRs with Receptor Activity-Modifying Proteins

description: Receptor activity-modifying proteins (RAMPs) have been described to form complexes with G protein-coupled receptors (GPCRs). Here, we present a comprehensive <b>GPCR-RAMP interactome</b> based on a library of 215 Dual Epitope-Tagged (DuET) GPCRs representing all GPCR subfamilies and co-expressed each GPCR with each of the three RAMPs.<b>The provided data describes multiplexed affinity-based measurements of the GPCRs and RAMPs.</b>The GPCRs were engineered to carry 1D4 and FLAG epitope tags, while the RAMPS carried OLLAS and HA tags. The receptors were co-overexpressed in Expi293F cells and solubilized for the interaction assays using Luminex's suspension bead array (SBA) technology. The platform is based on color-coded beads to distinguish the different assays. GPCRs and/or RAMPs were captured by antibodies on the beads, and another fluorescently labeled antibody was used for detection. The epitope tag capture and detection combinations allowed us to determine the interactions between GPCRs and RAMPs. We also used antibodies validated for GPCRs and RAMPs from a previous study (10.1126/sciadv.aaw2778) with open-access data (10.17044/scilifelab.21907995).The resulting output data are the median fluorescence intensity (MFI) values for each sample and bead. MFI represents a relative measurement of the receptors being captured by the antibody-conjugated beads. The submission also contains the data processed by Z-scores and robust Z-scores.<b>The resource also contains data from</b>a small pilot study to test the system,interaction SBA-screening of untransfected cells,interaction analysis in native membranes from the MolBoolean assay (https://doi.org/10.1038/s41467-022-32395-w).<b>File descriptions (version 2024-05-29)</b>`antibodies.csv` contains information about antibodies used in the GPCR-RAMP interaction overexpression screen.`endog_antibodies.csv` contains information about antibodies used in the screen for endogenous interactions.`endog_mfi.csv` contains data (signal-to-background ratios of MFI) for the assays of the endogenous interaction screening.`endog_well_info.csv` contains sample information for the assays of the endogenous interaction screening.`long_data.csv` contains sample information and measurements (MFI, Z-scores, and robust Z-scores) for samples in the GPCR-RAMP interaction over-expression screen.`molboolean.xlsx` contains measurements (RCPs/cell) from the MolBoolean native membrane interaction assays.`pilot_plate.xlsx` contains sample info and measurements (MFI) from a small-scale pilot plate for GPCR-RAMP interactions.<br>
DOI: 10.7483/opendata.cms.lh9j.5njr
title: /TprimeBToTH_TLep_Hbb_LH_MT900_MH100_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.25050422
title: Proteome profiling of home-sampled dried blood spots reveals proteins of SARS-CoV-2 infections

description: The report contains data on protein levels obtained from dried blood spot (DBS) samples.The DBS originated from donors who provided self-sampling blood using a sampling kit (Capitainer AB). The studies were conducted in the general population in Stockholm and Gothenburg (Sweden) during the COVID-19 pandemic in the spring of 2020 and 2021:Levels of <b>circulating </b><b>antibodies</b> were determined in the 2021 study by multi-analyte serology using the Luminex platform. Serology data from the 2020 studies have been deposited in a previous submission. All data sets have been processed and normalized using a linear model described in the publication of the previous submission.Levels of <b>circulating proteins</b> were determined by proximity extension assays using three Target96 panels from the Olink platform. The raw NPX data has been processed using AbsPQN, as described in the manuscript related to this submission.Other data is provided in the manuscript.Access to this individual-level human data can be granted for <b>non-commercial </b><b>v</b><b>alidation purposes</b> and upon reasonable request to the provided contact. A reasonable request should contain the following:Name of PI and host organizationContact detailsThe scientific purpose of the data access requestCommitment to inform when the data has been used in a publicationCommitment not to host or share the data outside the requesting organizationStatement of non-commercial use of data<br>
DOI: 10.7483/opendata.cms.j82w.v2oz
title: /TprimeBToTH_TLep_Hbb_LH_MT900_MH100_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.25050422.v1
title: Proteome profiling of home-sampled dried blood spots reveals proteins of SARS-CoV-2 infections

description: The report contains data on protein levels obtained from dried blood spot (DBS) samples.The DBS originated from donors who provided self-sampling blood using a sampling kit (Capitainer AB). The studies were conducted in the general population in Stockholm and Gothenburg (Sweden) during the COVID-19 pandemic in the spring of 2020 and 2021:Levels of <b>circulating </b><b>antibodies</b> were determined in the 2021 study by multi-analyte serology using the Luminex platform. Serology data from the 2020 studies have been deposited in a previous submission. All data sets have been processed and normalized using a linear model described in the publication of the previous submission.Levels of <b>circulating proteins</b> were determined by proximity extension assays using three Target96 panels from the Olink platform. The raw NPX data has been processed using AbsPQN, as described in the manuscript related to this submission.Other data is provided in the manuscript.Access to this individual-level human data can be granted for <b>non-commercial </b><b>v</b><b>alidation purposes</b> and upon reasonable request to the provided contact. A reasonable request should contain the following:Name of PI and host organizationContact detailsThe scientific purpose of the data access requestCommitment to inform when the data has been used in a publicationCommitment not to host or share the data outside the requesting organizationStatement of non-commercial use of data<br>
DOI: 10.17044/scilifelab.25186151
title: <b>Quantifying Fluorescence Lifetime Responsiveness of Environment-Sensitive Probes for Membrane Fluidity Measurements</b>

description: It contains data sets from Ragaller et al, Journal of Physical Chemistry B, 2024 (https://doi.org/10.1021/acs.jpcb.3c07006)It contains emission spectra, decay curves, lifetime images and excel sheets of the data.<b>Abstract</b>: The structural diversity of different lipid species within the membrane defines its biophysical properties such as membrane fluidity, phase transition, curvature, charge distribution and tension. Environment-sensitive probes, which change their spectral properties in response to their surrounding milieu, have greatly contributed to our understanding of such biophysical properties. To realize the full potential of these probes and to avoid misinterpretation of their spectral responses, a detailed investigation of their fluorescence characteristics in different environments is necessary. Here, we examined fluorescence lifetime of two newly developed membrane order probes, NR12S and NR12A, in response to alterations in their environments such as degree of lipid saturation, cholesterol content, double bond position and configuration and phospholipid headgroup. As comparison, we investigated lifetime sensitivity of the membrane tension probe Flipper in these environments. Applying fluorescence lifetime imaging microscopy (FLIM) in both model membranes and biological membranes, all probes distinguished membrane phases by lifetime, but exhibited different lifetime sensitivities to varying membrane biophysical properties (e.g. cholesterol). While the lifetime of Flipper is particularly sensitive to membrane cholesterol content, NR12S and NR12A lifetime is moderately sensitive to both cholesterol content and lipid acyl chains.<i> </i>Moreover, all probes exhibit longer lifetimes at longer emission wavelengths in membranes of any complexity. This emission-wavelength dependency results in varying lifetime resolution at different spectral regions, highly relevant for FLIM data acquisition. Our data provides valuable insights on how to perform FLIM with these probes and highlights both their potential and limitations.<b>Data usage</b>Researchers are welcome to use the data contained in the dataset for any projects. Please cite this item upon use or when published. We encourage reuse using the same CC BY 4.0 License.<b>Data Content</b>png or tif files for lifetime imagesExcel files for graphs<br><b>Software to open files</b>.xlsx - Microsoft Excel.tif, .png - Fiji (https://imagej.net/Fiji.html#Downloads)
DOI: 10.17044/scilifelab.25186151.v1
title: <b>Quantifying Fluorescence Lifetime Responsiveness of Environment-Sensitive Probes for Membrane Fluidity Measurements</b>

description: It contains data sets from Ragaller et al, Journal of Physical Chemistry B, 2024 (https://doi.org/10.1021/acs.jpcb.3c07006)It contains emission spectra, decay curves, lifetime images and excel sheets of the data.<b>Abstract</b>: The structural diversity of different lipid species within the membrane defines its biophysical properties such as membrane fluidity, phase transition, curvature, charge distribution and tension. Environment-sensitive probes, which change their spectral properties in response to their surrounding milieu, have greatly contributed to our understanding of such biophysical properties. To realize the full potential of these probes and to avoid misinterpretation of their spectral responses, a detailed investigation of their fluorescence characteristics in different environments is necessary. Here, we examined fluorescence lifetime of two newly developed membrane order probes, NR12S and NR12A, in response to alterations in their environments such as degree of lipid saturation, cholesterol content, double bond position and configuration and phospholipid headgroup. As comparison, we investigated lifetime sensitivity of the membrane tension probe Flipper in these environments. Applying fluorescence lifetime imaging microscopy (FLIM) in both model membranes and biological membranes, all probes distinguished membrane phases by lifetime, but exhibited different lifetime sensitivities to varying membrane biophysical properties (e.g. cholesterol). While the lifetime of Flipper is particularly sensitive to membrane cholesterol content, NR12S and NR12A lifetime is moderately sensitive to both cholesterol content and lipid acyl chains.<i> </i>Moreover, all probes exhibit longer lifetimes at longer emission wavelengths in membranes of any complexity. This emission-wavelength dependency results in varying lifetime resolution at different spectral regions, highly relevant for FLIM data acquisition. Our data provides valuable insights on how to perform FLIM with these probes and highlights both their potential and limitations.<b>Data usage</b>Researchers are welcome to use the data contained in the dataset for any projects. Please cite this item upon use or when published. We encourage reuse using the same CC BY 4.0 License.<b>Data Content</b>png or tif files for lifetime imagesExcel files for graphs<br><b>Software to open files</b>.xlsx - Microsoft Excel.tif, .png - Fiji (https://imagej.net/Fiji.html#Downloads)
DOI: 10.7483/opendata.cms.rz61.4yps
title: /TprimeBToTH_TLep_Hbb_LH_MT900_MH125_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.25237765
title: Plasma proteomics in two Swedish Ovarian Cancer cohorts

description: Plasma samples of women with benign and malignant ovarian tumors were collected from either the U-CAN collection<sup> </sup>at Uppsala Biobank, Sweden or the Gynaecology tumor biobank Göteborg, Sweden. All samples from the biobanks were included based on surgical ovarian cancer diagnosis or patients that had been surgically diagnosed with benign conditions based on suspicion of ovarian cancer. Exclusion criteria were patients that had received neoadjuvant treatment prior to surgery or if the tumor was pathologically determined to be metastatic originating from other tissues. The samples from Uppsala were collected between 2012 and 2018. The samples from Göteborg were collected from 2016 to 2018. The tumors were examined by pathologist specialized in gynaecologic cancers for histology, grade, and stage according to International Federation of Gynaecology and Obstetrics (FIGO) standards.The samples used here have previously been analyzed with the proximity extension assay (PEA)<sup> </sup>Explore1536 assay (Gyllensten, U. <i>et al.</i> Next Generation Plasma Proteomics Identifies High-Precision Biomarker Candidates for Ovarian Cancer. <i>Cancers (Basel) </i>14, 1757 (2022), Bueno Álvez, M. <i>et al.</i> Next generation pan-cancer blood proteome profiling using proximity extension assay. Nature Communications 14, 4308 (2023)) and was here complemented with the PEA Explore3072. The samples were randomized across seven 96 well plates. Protein concentrations are reported in NPX (normalised protein expression). The NPX data are on a log2 scale and in the logarithmic phase of the curve one increase of the NPX value corresponds to a doubling of the protein content. A high NPX value corresponds to a high protein concentration. Each of the measured proteins has a lower limit of detection (LOD) which is determined at run time. Here, each protein measure with NPX under LOD was replaced with the plate-specific LOD as indicated in the provided result file from the manufacturer. In total 2493 unique proteins were measured in up to 521 individuals. The study was approved by the Regional Ethics Committee in Uppsala (Dnr: 2016/145) and Göteborg (Dnr: 201-15) and informed written consent was obtained from all participants following the guidelines of the Declaration of Helsinki.<br><br>
DOI: 10.7483/opendata.cms.wue6.9xzd
title: /TprimeBToTH_TLep_Hbb_LH_MT900_MH125_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.7483/opendata.cms.qilr.sv4e
title: /TprimeBToTH_TLep_Hbb_LH_MT900_MH150_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.25315867
title: Supplementary data associated with two publications contrasting gene expression during somatic and zygotic embryo development and identifying long intergenic non coding RNAs during somatic embryogenesis

description: RNA-Seq data was generated from stages of somatic (SE) and zygotic embryogenesis (ZE). The developing zygotes (Zem) were isolated from the female megagametyophyte (FG) tissue at later stages. Differential expression analysis was performed for each dataset and the results were compared to identify common and contrasting expression changes.The somatic embryogenesis data was used to predict long intergenic RNAs and a co-expression network was generated. The network was used to assign putative functional annotation to the lincRNAs using a guilt-by-association approach.The normalised expression values, results of differential expression test, results of functional enrichment of gene sets and figures representing these are included. The sequences of identified lncRNAs are included as well as annotation information.The data is structured in three folders:<br><br>SE = Somatic Embryogenesis<br>ZE = Zygotic Embryogenesis<br>SE_ZE = All files related to the comparison of differentially expressed genes between the two datasets.<br><br>Some of the file names or figures can contain abbreviations different from the ones in the original publications. A conversion table is provided in the README file. More information on the folder and file content can be found in the manifest file.<br>
DOI: 10.17044/scilifelab.25315867.v2
title: Supplementary data associated with two publications contrasting gene expression during somatic and zygotic embryo development and identifying long intergenic non coding RNAs during somatic embryogenesis

description: RNA-Seq data was generated from stages of somatic (SE) and zygotic embryogenesis (ZE). The developing zygotes (Zem) were isolated from the female megagametyophyte (FG) tissue at later stages. Differential expression analysis was performed for each dataset and the results were compared to identify common and contrasting expression changes.The somatic embryogenesis data was used to predict long intergenic RNAs and a co-expression network was generated. The network was used to assign putative functional annotation to the lincRNAs using a guilt-by-association approach.The normalised expression values, results of differential expression test, results of functional enrichment of gene sets and figures representing these are included. The sequences of identified lncRNAs are included as well as annotation information.The data is structured in three folders:<br><br>SE = Somatic Embryogenesis<br>ZE = Zygotic Embryogenesis<br>SE_ZE = All files related to the comparison of differentially expressed genes between the two datasets.<br><br>Some of the file names or figures can contain abbreviations different from the ones in the original publications. A conversion table is provided in the README file. More information on the folder and file content can be found in the manifest file.<br>
DOI: 10.17044/scilifelab.25323256
title: <b>Human adaptation in the Andes Mountains</b>

description: This dataset contains genome-wide single nucleotide polymorphism (SNP) genotype data generated from 81 individuals (78 women and 3 men of Aymara-Quecha and Uru ethnicities) from the Bolivian Altiplano and 32 women from the Argentinean Puna (Atacameño-Kolla ethnicity). DNA was extracted from whole blood samples or buccal cells with EZNA Blood DNA Mini kit (Omega Bio-teck, USA) or Qiagen Blood Mini kit (Qiagen, Germany). Genome-wide genotyping was performed at the SNP&Seq Technology Platform in Uppsala (Sweden) on the Illumina Infinium Omni5Exome and on the Illumina Infinium Omni5M bead chips for the Bolivian and Argentinean study groups, respectively. The data was aligned to the human reference genome build, version 37 (hg19).<br>This metadata record contains information of 162 IDAT files generated from the Illumina Infinium Omni5Exome and on the Illumina Infinium Omni5M arrays, and 3 PLINK files (bim, bam and fam). The data takes 10GB of storage.Terms for access:<br>· The genome-wideSNP genotype dataset is only to be used for research that is seeking to advance the understanding of the human adaptation to extreme environments.· The data should not be used for other purposes, i.e. investigating the genetic signatures that may lead to identification of a person.· Not to use this data or any part thereof for the creation of products or services for sale or to sale the data or parts of the data or to use the data for any commercial purpose.· Do not to transfer or disclose the data, in whole or part, or any identifiable material derived from the data, to third parties or persons not directly involved in the research.· Preserve, at all times, the confidentiality of information and data pertaining to sample donors. In particular, not to use, or attempt to use the data to compromise or otherwise infringe the confidentiality of information of the sample donors and their right to privacy.· Not to use the information included in the data to identify the data subjects nor to contact them under any circumstances.· Any work based in whole or part on the data shall acknowledge the published paper from which the data derives.
DOI: 10.7483/opendata.cms.ld7b.qa9j
title: /TprimeBToTH_TLep_Hbb_LH_MT900_MH150_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.25334122
title: Genotyping data from 209 Swedish Labrador retrievers

description: Genotyping data from 209 Labrador retrievers from genome wide association study investigating genetic risk factors for hip dysplasia within the breed. In addition data has also been used to investigate association with body weight in female Labrador retrievers.
DOI: 10.17044/scilifelab.25334122.v1
title: Genotyping data from 209 Swedish Labrador retrievers

description: Genotyping data from 209 Labrador retrievers from genome wide association study investigating genetic risk factors for hip dysplasia within the breed. In addition data has also been used to investigate association with body weight in female Labrador retrievers.
DOI: 10.7483/opendata.cms.kfz5.ji4l
title: /TprimeBToTH_TLep_Hbb_LH_MT900_MH175_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.25335448
title: Data for the <i>Populus tremula</i> v2.2. genome project and associated genome-wide association study

description: <b>Background to the study:</b> We have produced a chromosome-scale genome assembly generated using long-read sequencing, optical and high-density genetic maps containing 39,894 annotated genes with functional annotations for 73,765 transcripts in 37,184 genes. We conducted whole-genome resequencing of the Umeå Aspen (UmAsp) collection comprising 227 aspen individuals. We utilised the assembly and existing whole genome re-sequencing data to perform genome-wide association<i> </i>analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) in the UmAsp, Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections for leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq) and identified genomic regions of accessible chromatin, and subset SNPs to these regions, which improved the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples and quantified their expression in an updated co-expression network, which we used to explore the functions of candidate genes identified from the GWAS.<br><br><b>This data set comprises: </b>the ATAC-Seq peaks from the ATAC-Sequencing of aspen leaves, '<b>Aspen leaf ATAC_Seq peaks</b><b>.zip'</b>; and the gene expression matrix of mean values per aspen genotype from the SwAsp collection, '<b>Gene_Expression_matrix_genotype_mean.tsv'</b>. We provide a zipped directory for each of '<b>ScotAsp.zip'</b>, '<b>SwAsp.zip'</b> and '<b>UmAsp.zip'</b> providing the raw leaf image scans, the cropped leaf images and raw data files from the LAMINA leaf shape analyses of these images, and the processed data files and genotypic BLUP values for each of these ScotAsp, SwAsp and UmAsp collections. We provide the GWAS associations of SNPs ranked by decreasing P-value until the 1000th gene for each of the 26 leaf physiognomy traits for each collection, i.e. '<b>ScotAsp top-ranked GWAS results'</b><b>, '</b><b>SwAsp top-ranked GWAS</b><b> results'</b> and '<b>Um</b><b>Asp top-ranked GWAS results'</b>. The single nucleotide polymorphism (SNP) data for each of the aspen collections is in <b>'</b><b>ScotAsp_biallelic_Het.HWE.recode.vcf</b><b>.gz</b><b>'</b><b>, 'SwAsp_AfterBatchRemoval_biallelic_Het.HWE.recode.vcf.gz' </b>and<b> 'UmAsp_biallelic_Het.MAF.HWE.recode_.vcf.gz'.</b>