88 Works

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...

BAGS.v1

Luis Fernando Delgado Zambrano & Anders Andersson
The BAltic Gene Set (BAGS.v1) gene catalogue encompasses 67,566,251 genes. The 67 million genes are based on 124 metagenome samples from seawater that span the salinity and oxygen gradients of the Baltic Sea and also capture seasonal dynamics at two locations. To obtain the gene catalogue, we used a mix-assembly approach. In short, mix-assembly is performed in three steps: 1) assembly on individual samples followed by gene calling and clustering of the resulting genes in...

BAGS.v1: BAltic Gene Set gene catalogue

Luis Fernando Delgado Zambrano & Anders Andersson
The BAltic Gene Set (BAGS.v1) gene catalogue encompasses 67,566,251 genes. The 67 million genes are based on metagenomic data from Alneberg at al. (2020) from 124 seawater samples that span the salinity and oxygen gradients of the Baltic Sea and capture seasonal dynamics at two locations. To obtain the gene catalogue, we used a mix-assembly approach described in Delgado et al. (2021). The gene catalogue has been functionally and taxonomically annotated, as described in Delgado...

Docking Results

Gabriele Pozzati, Petras Kundrotas & Arne Elofsson
Results for the study "Improved protein docking by predicted interface residues". Archive contains GRAMM roto-translations of Ligands around the original position of the Receptor. Several set of docking models have been produced considering different set of protein interface constraintsto score GRAMM roto-translations. Also, AACE18 scoring function results are included. For every docking model, DockQ score has been calculated comparing with both bound and unbound native structures. Find detailed methods at https://www.biorxiv.org/content/10.1101/2021.08.25.457642v1

Docking Results

Gabriele Pozzati, Petras Kundrotas & Arne Elofsson
Results for the study "Improved protein docking by predicted interface residues". Archive contains GRAMM roto-translations of Ligands around the original position of the Receptor. Several set of docking models have been produced considering different set of protein interface constraintsto score GRAMM roto-translations. Also, AACE18 scoring function results are included. For every docking model, DockQ score has been calculated comparing with both bound and unbound native structures. Find detailed methods at https://www.biorxiv.org/content/10.1101/2021.08.25.457642v1

Autoantibody profiles associated with clinical features in psychotic disorders

August Jernbom Falk, Cherrie Galletly, David Just, Catherine Toben, Bernhard Baune, Scott Clark, Dennis Liu, Peter Nilsson, Anna Månberg & Oliver Schubert
Dataset from Jernbom Falk, A., Galletly, C., Just, D. et al. Autoantibody profiles associated with clinical features in psychotic disorders. Transl Psychiatry 11, 474 (2021).
Abstract:Autoimmune processes are suspected to play a role in the pathophysiology of psychotic disorders. Better understanding of the associations between auto-immunoglobulin G (IgG) repertoires and clinical features of mental illness could yield novel models of the pathophysiology of psychosis, and markers for biological patient stratification. We undertook cross-sectional detection and quantification...

Protein models for \"Towards a structurally resolved human protein interaction network\"

Arne Elofsson, Petras Kundrotas, Pedro Beltrao, Patrick Bryant & Gabriele Pozzati
Dataset descriptionThis is all prediction associated with the paper entitled 'Towards a structurally resolved human protein interaction network'.
Predicted protein models for 65000 human protein-protein interactions. Five datasets pairs: HuRUm HuMap2, Random single chain: HuRI and HuMap.
Additional resources can be found here: https://archive.bioinfo.se/huintaf2/Protein interaction data and annotationsHuman protein pairs known to physically interact were obtained from the Hu.MAP dataset, retaining pairwise interactions with >=0.5 confidence, and most interactions from the HuRI dataset.Protein complex predictionTo predict protein...

SPARC single-cell protein data

Johan Reimegård
This data set contains protein measurements from single cell and 100 cells from early human neural differentiation cells. Cells were harvested at time points 0 h, 24 h and 48 h.
Protein data measurements were carried out using PEA and quantitative values on protein concentrations were measures using qPCR. Following the completion of the qPCR run we visually inspected the amplification curves. Samples showing evidence of failed or poor amplification reactions were excluded from further analysis....

Immunofluorescence data of 700 host cell proteins in Sars-CoV2 infected vs non-infected VeroE6 cells

Jayasankar Mohanakrishnan Kaimal, Ulrika Axelsson, Trang H. Le, Marianna Tampere, Hao Xu, Hanna Axelsson, Anna Bäckström, Duncan Njenda, Elisabeth Moussaud-Lamodière, Wei Ouyang, Carolina Oses Sepulveda, Brinton Seashore-Ludlow, Caroline Vernersson, Ali Mirazimi, Päivi Östling, Emma Lundberg & Charlotte Stadler
The data set contains ≈ 75,000 confocal images of mixed Vero E6 cell populations (SARS-CoV2 infected vs non-infected). Cells had been infected with the virus for 1 h and fixed 24 hour post infection in 96 well plates. Using immunofluorescence (4 colours) cells were stained for the SARS-CoV2 virus (red), the endoplasmic reticulum (yellow) and nucleus (blue) – same for all images in the data set and used as reference markers. On top of this,...

Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma

Lucia Pena-Perez & Robert Månsson
This repository contains 10x Chromium linked-read WGS (lrWGS), RNAseq and H3K27Ac ChIPseq from multiple myeloma.
The data consists of fastq files from lrWGS of 37 individuals with data from tumor and matched normal tissue from 32 of them. Additionally, it contains fastq files from RNAseq of 32 of the 37 patients and H3K27Ac ChIPseq data from select patients.
The data set contains sensitive human genomic data and is under restricted access. Request for...

CSAW-M: An Ordinal Classification Dataset for Benchmarking Mammographic Masking of Cancer

Moein Sorkhei, Yue Liu, Hossein Azizpour, Edward Azavedo, Karin Dembrower, Dimitra Ntoula, Anthanasios Zouzos, Fredrik Strand & Kevin Smith
Welcome to the the CSAW-M dataset homepage
This page includes the files and metadata related to the CSAW-M, a curated dataset of mammograms with expert assessments of the masking of cancer. CSAW-M is collected from over 10,000 individuals and annotated with potential masking. In contrast to the previous approaches which measure breast image density as a proxy, our dataset directly provides annotations of masking potential assessments from five specialists. We trained deep learning models on CSAW-M...

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...

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...

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 Östhammar, Sweden

Anna Székely & Nahla Mohamed
This is a metadata record for a continuously updated dataset of SARS-CoV-2 RNA data in wastewater in Östhammar, 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 Östhammar, Sweden

Anna Székely & Nahla Mohamed
This is a metadata record for a continuously updated dataset of SARS-CoV-2 RNA data in wastewater in Östhammar, 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 in wastewater in Umeå, Sweden

Maja Malmberg, Mette Myrmel &
This is a metadata record for a continuously updated dataset of SARS-CoV-2 RNA data in wastewater in Umeå, 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 Umeå. The research group is...

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...

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...

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...

WGS in familial chronic lymphocytic leukemia

Viktor Ljungström & Richard Rosenquist Brandell
Data Set Description

This repository contains data from a study of three families in which two or more siblings developed chronic lymphocytic leukemia (CLL). Informed consent was provided in accordance with the declaration of Helsinki and the study was approved by the hospital medical ethics committee (METC2015-741).
The data consists of BAM-files from whole-genome sequencing (WGS) of nine individuals with data from tumor and matched normal tissue. WGS libraries where prepared using the TruSeq Nano Kit (Illumina...

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 for: Sequence specificity in DNA binding is mainly governed by association

Emil Marklund, Guanzhong Mao, Jinwen Yuan, Spartak Zikrin, Eldar Abdurakhmanov, Sebastian Deindl & Johan Elf
Sequence-specific binding of proteins to DNA is essential for accessing genetic information. Here, we derive a simple equation for target-site recognition, which uncovers a previously unrecognized coupling between the macroscopic association and dissociation rates of the searching protein. Importantly, this relationship makes it possible to recover the relevant microscopic rates from experimentally determined macroscopic ones. This post contains kinetic data for the lac repressor and code to analyse and interpret the data in light of...

Data and most relevant results for the FoldDock project

Patrick Bryant, Gabriele Pozzati & Arne Elofsson
Data and main results for the study "Improved prediction of protein-protein interactions using AlphaFold2 and extended multiple-sequence alignments."
Contained datasets consist of:1 - 219 heterodimers from dockground benchmark 4 dataset 2 - 1503 heterodimeric structures from a recent study (Green, A. G. et al. Nat. Commun. 12, 1–12 (2021))3 - 7 heterodimeric complexes from CASP144 - 8 novel heterodimeric complexes deposited in the PDB database after 15 June 2021
For each one of the mentioned datasets it...

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...

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  • 2021
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