88 Works

Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2

Niclas Roxhed, Annika Bendes, Matilda Dale, Cecilia Mattsson, Leo Hanke, Tea Dodig-Crnkovic, Christian Murray, Birthe Meineke, Simon Elsässer, Juni Andrell, Sebastian Haverall, Charlotte Thålin, Carina Eklund, Joakim Dillner, Olof Beck, Cecilia Engel Thomas, Gerald M. McInerney, Mun-Gwan Hong, Ben Murrell, Claudia Fredolini & Jochen Schwenk
Dried blood spot (DBS) samples were collected during spring of 2020 from random and undiagnosed individuals in Stockholm, Sweden.
Receiving DBS from 878 participants, we applied multiplexed serology assays to determine IgG and IgM levels against several versions of SARS-CoV-2 proteins (S, RBD, N).
The data reports anonymised an normalised "relative antibody titers" obtained in the eluates of the DBS samples. The data can be made available for validation purposes and upon reasonable request.
A reasonable...

Dataset of SARS-CoV-2 wastewater data from Uppsala, Sweden

Anna Székely & Nahla Mohamed
This is a metadata record for a continuously updated dataset of SARS-CoV-2 RNA data in wastewater in Uppsala, Sweden.
The dataset is part of a research study led associate professor Anna J. Székely (SLU, Swedish University of Agricultural Sciences) and her research groups in collaboration with Uppsala Vatten. The research group is part of the Environmental Virus Profiling Research Area of the SciLifeLab National COVID-19 Research Program.
The viral content is concentrated according to the protocol...

Detailed feature profile of MapToCleave processed and unprocessed miRNA precursors

Wenjing Kang, Bastian Fromm, Inna Biryukova & Marc Friedländer
This is the Supplemental Data 6 of the MapToCleave study.
The file folder contains detailed feature information of MapToCleave processed and unprocessed miRNA precursors. There are seven feature files for each miRNA precursor. The file with the suffix “.HEK.statistics” provides basic information on the hairpin. The file with the suffix “.fold” provides RNA secondary structure in dot bracket format predicted by RNAfold. The file with the suffix “.str” provides printed RNA secondary structure in txt...

Dataset for \"Serological and molecular study of Crimean-Congo hemorrhagic fever virus in cattle from selected districts in Uganda\" _serology_25012021

Stephen Balinandi, Claudia Von Brömssen, Alex Tumusiime, Jackson Kyondo, , Vanessa Monteil, Ali Mirazimi, Julius Lutwama, Lawrence Mugisha & Maja Malmberg

DATASET This dataset presented is a summary of information about the animals and test results that are reported in the Manuscript, ‘Serological and Molecular Study of Crimean-Congo Hemorrhagic Fever Virus in cattle from selected districts in Uganda’. Below is an explanation text on some of the data variables and acronyms found in the file. A: BIODATA WORKSHEET contains information about number, code, district, sub county, parish, village and GPS location of where study samples were...

Dataset of bibliographic information about publications on COVID-19 and SARS-CoV-19 by researchers affiliated with a university or research institute in Sweden

Katarina Öjefors Stark &
This is a metadata record for a continuously updated dataset of preprints and journal articles on SARS-CoV-2 and COVID-19 where at least one author has an affiliation with a Swedish university or research institute. The dataset is created as part of the Swedish COVID-19 Data Portal (https://covid19dataportal.se). The dataset is manually curated.
The most recent version can be browsed using the following link: https://covid19dataportal.se/publications/.
The most recent version can be downloaded as a .JSON file using...

Data used in exercises in course Introduction to Data Management Practices

Yvonne Kallberg, Elin Kronander, Niclas Jareborg, Markus Englund &
This record contains the data files used in exercises in the NBIS course "Introduction to Data Management Practices".

PRONMED Uppsala COVID-19 ICU Biobank

Michael Hultström, Robert Frithiof & Miklós Lipcsey
The dataset consists clinical data and biobankes samples from 250 critically ill COVID-19 patients admitted to intensive care at Uppsala University Hospital.
During intensive care patients are sampled during weekdays. Wholeblood is collected for DNA sequencing. EDTA- and citrate-plasma, with corresponding cell pellets as well as urine is collected and frozen at -80°C until further use. In addition, PBMCs, PAX tubed for RNA-stabilized blood, and CyTOF tubes for single cell proteomics are collected and frozen. At...

How Does Liquid-Liquid Phase Separation in Model Membranes Reflect Cell Membrane Heterogeneity?

Erdinc Sezgin & Taras Sych
It contains figures from Sych et al, Membranes, 2021.
First figure shows visualization of phase separation in synthetic and cell-derived membrane systems using phase selective probesSecond figure shows membrane order in liquid-ordered and liquid-disodered phases of synthetic and cell-derived membranes.Figures are provided in Inkscape svg format. Images are taken with confocal microscopy, and generalized polarization map was generated by using custom FiJi software (Sezgin et al, ChemPhysChem, 2015).

## Abstract of the paper
Although liquid–liquid phase...

Data for ''RecA finds homologous DNA by reduced dimensionality search’

Jakub Wiktor, Arvid Heden Gynnå, Prune Leroy, Jimmy Larsson, Giovanna Coceano, Ilaria Testa & Johan Elf
### Dataset description
The data here is provided to support the publication 'RecA finds homologous DNA by reduced dimensionality search’. The supporting data is largely of two types: (1) Image sequences from automated widefield microscopy of live cells in a microfluidic device, and (2) STED superresolution images of fixed and immunostained cells

For automated widefield microscopy, the 'data' folder contains the raw microscopy images, together with the output from the image processing pipeline - stabilised and...

Data used in exercises in course Introduction to Data Management Practices

Yvonne Kallberg, Elin Kronander, Niclas Jareborg, Markus Englund &
This record contains the data files used in exercises in the NBIS course "Introduction to Data Management Practices".

IPR0220 - InterPepRank set

Isak Johansson-Åkhe, Claudio Mirabello & Björn Wallner
Peptide-protein interactions between a smaller or disordered peptide stretch and a folded receptor make up a large part of all protein-protein interactions. A common approach for modelling such interactions is to exhaustively sample the conformational space by fast-fourier-transform docking, and then refine a top percentage of decoys. Commonly, methods capable of ranking the decoys for selection in short enough time for larger scale studies rely on first-principle energy terms such as electrostatics, Van der Waals...

Swedish National study on Aging and Care in Kungsholmen (SNAC-K) COVID-19 Study

Laura Fratiglioni, Giorgi Beridze & Amaia Calderón-Larrañaga
Abstract These data are collected from 1428 older adults aged 60 and above. The project is embedded in the ongoing Swedish National Study on Aging and Care in Kungsholmen (SNAC-K), a population-based study with regular health assessments since 2001. https://www.snac-k.se/
The SNAC-K COVID-19 study aims to: 1) Estimate the short-term collateral damage on older adults’ health during the first months of the COVID-19 outbreak; 2) Detect the long-term collateral repercussions on older adults health up to...

Dataset of SARS CoV-2 in wastewater in Örebro, Sweden

Maja Malmberg, Mette Myrmel &
This is a metadata record for a continuously updated dataset of SARS-CoV-2 RNA data in wastewater in Örebro, Sweden.The dataset is part of a research study led by associate professor Maja Malmberg (SLU, Swedish University of Agricultural Sciences) and her research group in collaboration with associate professor Mette Myrmel at the Norwegian University of Life Sciences.
The amount of SARS-CoV-2 virus is measured in wastewater from the wastewater treatment facility in Örebro. The research group...

Data from: Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets

Linda Holmfeldt & Svea Stratmann

Data Set Description
These data are collected from a total of 73 participants (48 adult; 25 pediatric), all of which had relapsed or primary resistant acute myeloid leukemia. The data, which here are separated into an adult and a pediatric dataset, were generated as part of a study by Stratmann et. al., 2021 (https://doi.org/10.1182/bloodadvances.2020003709).
Please note that separate applications are necessary for the adult and pediatric dataset, respectively. When applying for access, please indicate which of the...

PRONMED Uppsala COVID-19 ICU Biobank

Michael Hultström, Robert Frithiof & Miklós Lipcsey
The dataset consists clinical data and biobankes samples from 250 critically ill COVID-19 patients admitted to intensive care at Uppsala University Hospital.
During intensive care patients are sampled during weekdays. Wholeblood is collected for DNA sequencing. EDTA- and citrate-plasma, with corresponding cell pellets as well as urine is collected and frozen at -80°C until further use. In addition, PBMCs, PAX tubed for RNA-stabilized blood, and CyTOF tubes for single cell proteomics are collected and frozen. At...

COMMUNITY study

Charlotte Thålin, Sophia Hober, Mia Phillipson, Sara Mangsbo & Peter Nilsson
Datasets from COMMUNITY study including 2149 healthcare workers. Longitudinal cohort study. Data include1. Data from serological analysis HCW n=2149 and patients n=118 at baseline and HCW n=1974 and patients n=59 at four-month follow-up.Raw data from IgG antibodies against various epitopes on the SARS-CoV-2 virus.

2. Raw data from collected self-report questionnaire (N=2149) investigating predefined prior symptoms compatible with COVID-19 since 1 January 2020, occupation, work location and self-reported exposure to patients infected with COVID-19 prior to...

Data from: A systems biology approach identifies B cell maturation antigen (BCMA) as biomarker reflecting oral vaccine induced IgA antibody responses in humans

Lynda Mottram, Anna Lundgren, & Susannah Leach
In this study, RNA-Seq was performed on peripheral blood mononuclear cells (PBMCs) isolated from six volunteers of a oral cholera Dukoral® vaccine study performed by Mottram et al., 2020.(10.1016/j.vaccine.2019.10.050).
The raw FASQ and indexed aligned BAM files described here were taken from four strong and two non IgA antibody responders of this Dukoral® vaccine study and are part of another study described by Mottram et al (2021) (Frontiers in Immunology, accepted for publication).
Total...

SARS-CoV-2 Wastewater Data from Stockholm, Sweden

Zeynep Cetecioglu Gurol, Cecilia Williams, Kasra Khatami, Merve Atasoy, Prachi Nandy, Mohammed Hakim Jafferali & Madeleine Birgersson
The dataset is part of a research study lead by associate professor Zeynep Cetecioglu Gurol and colleagues (KTH Royal Institute of Technology), is a collaboration between the SciLifeLab COVID-19 National Research Program and Chemical Engineering and Protein Science departments at KTH, in close collaboration with Stockholm Vatten och Avfall and the Käppala Association.
The sampling of wastewater, started in mid-April 2020, from Bromma, Henriksdal, and Käppala wastewater treatment plants (WWTP). These treatment plants receive wastewater from...

Dataset of SARS-CoV-2 wastewater data from Enköping, Sweden

Anna Székely & Nahla Mohamed
This is a metadata record for a continuously updated dataset of SARS-CoV-2 RNA data in wastewater in Enköping, Sweden.
The dataset is part of a research study led associate professor Anna J. Székely (SLU, Swedish University of Agricultural Sciences) and her research groups in collaboration with Uppsala Vatten. The research group is part of the Environmental Virus Profiling Research Area of the SciLifeLab National COVID-19 Research Program.
The viral content is concentrated according to the protocol...

Dataset of SARS-CoV-2 wastewater data from Knivsta, Sweden

Anna Székely & Nahla Mohamed
This is a metadata record for a continuously updated dataset of SARS-CoV-2 RNA data in wastewater in Knivsta.
The dataset is part of a research study led associate professor Anna J. Székely (SLU, Swedish University of Agricultural Sciences) and her research groups in collaboration with Uppsala Vatten. The research group is part of the Environmental Virus Profiling Research Area of the SciLifeLab National COVID-19 Research Program.
The viral content is concentrated according to the protocol from Ahmed...

A phenomics approach for antiviral drug discovery - Images, analysis pipelines and feature data

Jonne Rietdijk, Marianna Tampere, Aleksandra Pettke, Polina Georgieva, Maris Lapins, Ulrika Warpman Berglund, Ola Spjuth, Marjo-Riitta Puumalainen & Jordi Carreras Puigvert
Abstract:

The current COVID-19 pandemic has highlighted the need for new and fast methods to identify novel or repurposed therapeutic drugs. Here we present a method for untargeted phenotypic drug screening of virus-infected cells, combining Cell Painting with antibody-based detection of viral infection in a single assay. We designed an image analysis pipeline for segmentation and classification of virus-infected and non-infected cells, followed by extraction of morphological properties. We show that the methodology can successfully capture...

A phenomics approach for antiviral drug discovery - Images, analysis pipelines and feature data

Jonne Rietdijk, Marianna Tampere, Aleksandra Pettke, Polina Georgieva, Maris Lapins, Ulrika Warpman Berglund, Ola Spjuth, Marjo-Riitta Puumalainen & Jordi Carreras Puigvert
Abstract:

The current COVID-19 pandemic has highlighted the need for new and fast methods to identify novel or repurposed therapeutic drugs. Here we present a method for untargeted phenotypic drug screening of virus-infected cells, combining Cell Painting with antibody-based detection of viral infection in a single assay. We designed an image analysis pipeline for segmentation and classification of virus-infected and non-infected cells, followed by extraction of morphological properties. We show that the methodology can successfully capture...

Detailed feature profile of MirGeneDB highly and lowly expressed miRNA precursors

Wenjing Kang, Bastian Fromm, Inna Biryukova & Marc Friedländer
This is the Supplementary Data 9 of the MapToCleave study. ​​The file folder contains detailed feature information of MirGeneDB highly and lowly expressed miRNA precursors of 20 species. There are six feature files for each miRNA precursor. The file with the suffix “.statistics” provides basic information on the hairpin. The file with the suffix “.fold” provides RNA secondary structure in dot bracket format predicted by RNAfold. The file with suffix “.unopened_5p_ref” and “.unopened_3p_ref” provides positional...

Dataset of SARS-CoV-2 wastewater data from Uppsala, and neighbouring towns Knivsta, Enköping, Östhammar and Älvkarleby, Sweden

Anna Székely & Nahla Mohamed
This is a metadata record for a continuously updated dataset of SARS-CoV-2 RNA data in wastewater in Uppsala and neighbouring towns Knivsta, Enköping, Östhammar and Älvkarleby.
The dataset is part of a research study led associate professor Anna J. Székely (SLU, Swedish University of Agricultural Sciences) and her research groups in collaboration with Uppsala Vatten. The research group is part of the Environmental Virus Profiling Research Area of the SciLifeLab National COVID-19 Research Program.
The viral content...

Human T cell scRNAseq

Joanna Hård & Jakob Michaelsson
This dataset contains genomic TCR beta sequences from single cell DNA samples amplified by multiple displacement amplification (MDA) and subjected to nested PCR targeting the genomic TCR beta locus. The individual files contain raw data representing nucleotide sequences including both productive and non-productive rearrangements of the TCR beta sequence (with dropout in some cases).
FASTQ files corresponding to single cell RNAseq data from single CD8+ T cells prepared by the smart-seq2 method.

FASTQ files for 25-cell...

Registration Year

  • 2021
    88

Resource Types

  • Dataset
    88