175 Works

HASTE miniTEM Example Images

Ben Blamey & Ida-Maria Sintorn
Series of images of a sample of kidney tissue captured from the miniTEM (a 25keV transmission electron microscope) at Vironova offices in Stockholm (2019-02-04), for purposes of testing software related to the HASTE project (http://haste.research.it.uu.se/).
The dataset consists of 759 8-bit greyscale PNG images.

Used in this publication (and others):
Resource- and Message Size-Aware Scheduling of Stream Processing at the Edge with application to Realtime MicroscopyBen Blamey, Ida-Maria Sintorn, Andreas Hellander, Salman Toorhttps://arxiv.org/abs/1912.09088
Also"Rapid development of cloud-native intelligent data...

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...

5PSeq analysis conecting translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae

Vicent Pelechano & Alisa Alekseenko
Supplementary information for the manuscript: A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae. 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
Here we provide browsable metagene analysis for 5´P mRNA degradation profiles.Raw and processed sequencing data are deposited at Gene Expression Omnibus...

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".

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...

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 and code related to \"Direct measurements of mRNA translation kinetics in living cells\", by Metelev et al.

Mikhail Metelev, Erik Lundin, Ivan L. Volkov, Arvid Heden Gynnå, Johan Elf & Magnus Johansson
This repository contains microscopy data and analysis code related to the publication: Metelev et al., "Direct measurements of mRNA translation kinetics in living cells".
The study includes single-particle tracking of ribosomal subunits in live E. coli cells, for analysis of translation kinetics under different conditions.
A detailed list of files and file organization can be found in the readme text file.

Single cell whole genome sequencing of high hyperdiploid acute lymphoblastic leukemia

Eleanor Woodward, Minjun Yang, Larissa Helena Moura-Castro, Hilda van den Bos, Rebeqa Gunnarsson, Linda Olsson Arvidsson, Diana C. J. Spierings, Anders Castor, Nicolas Duployez, Marketa Zaliova, Jan Zuna, Bertil Johansson, Floris Foijer & Kajsa Paulsson
This dataset was collected from viable bone marrow cells obtained at diagnosis from nine patients with high hyperdiploid ALL and one normal bone marrow sample. All samples were subjected to low pass single cell whole genome sequencing with the median sequencing coverage of 0.02x. Single nuclei in G0/G1 phase were isolated using a fluorescence-activated cell sorting (FACS) cytometer. DNA libraries were constructed and associated next-generation sequencing was carried out by European Research Institute for the...

Data from: Strong genetic, clinical and lifestyle effects on biomarker variation: towards the use of personalized cut-offs

Stefan Enroth, Åsa Johansson, Sofia Bosdotter Enroth & Ulf Gyllensten
Summary statistics from the GWAS on circulating plasma protein levels.

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...

Improved computational analysis of ribosome dynamics from 5’P degradome data using fivepeseq

Vicent Pelechano, Lilit Nersisyan & Maria Ropat
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)
Dataset updated to fivepseq version1.0b6

5'P mRNA degradome datasets analyzed with fivepseq. (http://pelechanolab.com/software/fivepseq/). Raw Saccharomyces cerevisiae data is available from GEO under accession code GSE91064 and for Arabidopsis thaliana under accessions GSE72505 and GSE77549.

Genotype data from: \"Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling.\"

Christian Lundtoft, Pascal Pucholt, Juliana Imgenberg-Kreuz, Jonas Carlsson Almlöf, , , Gunnel Nordmark, Johanna K. Sandling, Ingrid Kockum, Tomas Olsson, Lars Rönnblom & Niklas Hagberg
This data contains genotype data from the GlobalScreeningArray and imputed genotypes from 303 healthy blood donors, generated within a project to investigate pQTLs regulating interferon receptor responses.
Results are published in Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling (https://doi.org/10.1371/journal.pgen.1009199)

Abstract:Interferons (IFNs) are cytokines that are central to the host defence against viruses and other microorganisms. If not properly regulated, IFNs may contribute to the pathogenesis of...

SMCT-FCS data from DNA surface exploration and operator bypassing during target search

Emil Marklund, Brad Van Oosten, , Elias Amselem, Kalle Kipper, Anton Sabantsev, Andrew Emmerich, Daniel Globisch, Xuan Zheng, Laura Lehmann, Otto Berg, Magnus Johansson, Johan Elf & Sebastian Deindl
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.

Data from: Single cell analysis of autism patient with bi-allelic NRXN1-alpha deletion reveals skewed fate choice in neural progenitors and impaired neuronal functionality

Matti Lam, Malin Kele, Marcela Ferella, Anna Juréus, Peter Lönnerberg & Anna Falk

ACpop Variant Frequency Dataset

Matilda Rentoft, Daniel Svensson, Andreas Sjödin, Pall I. Olason, Andrei Chabes, Johan Trygg, Beatrice S. Melin & Erik Johansson

Duplex sequencing uncovers recurrent low-frequency cancer-associated mutations in KMT2A-rearranged infant acute leukemia

Mattias Pilheden & Anna Hagström Andersson
This dataset includes Duplex sequencing and targeted next generation sequencing (NGS) of 20 Infants and 7 Children with acute lymphoblastic leukmia. All patients had an underlying rearrangement of the KMT2A gene, either KMT2A::MLLT3 (n=5), KMT2A::AFF1 (n=12), KMT2A::MLLT1 (n=8) or KMT2A::MLLT10 (n=2). The median age of the cohort was 7 months. Diagnostic sample from peripheral blod (n=11) or bone marrow (n=16) underwent the duplex sequencing library preparation as described in https://doi.org/10.1073/pnas.1208715109 and sequenced on the NextSeq...

Registration Year

  • 2022
    37
  • 2021
    88
  • 2020
    36
  • 2019
    6
  • 2018
    2
  • 2017
    1
  • 2015
    3
  • 2014
    2

Resource Types

  • Dataset
    175