175 Works

COMMUNITY study

Charlotte Thålin, Sebastian Havervall, Ulrika Marking, Nina Greilert-Norin, Kim Blom, Max Gordon, Jonas Klingström, Peter Nilsson, Sophia Hober, Mia Phillipson, Sara Mangsbo & Mikael Åberg
The COMMUNITY pandemic surveillance cohort is a longitudinal cohort study including 2149 healthcare workers and 118 COVID-19 patients. Dataset includes: 1. Serological data at baseline April-May 2020 and at follow-up every four month (ongoing). 2. Data on memory T cell responses 3. Register data from Swedish vaccination register (VAL Vaccinera) and national communicable diseases register SmiNet (Public Health Agency of Sweden). 3. Self-reported symptoms compatible with COVID-19 since 1 January 2020, occupation, work location and...

Morphological profiling of environmental chemical combinations - images, pipelines, and features

Jonne Rietdijk, Tanya Aggarwal, Polina Georgiev, Maris Lapins, Jordi Carreras-Puigvert & Ola Spjuth
Abstract: Environmental chemicals are commonly studied one at a time, and there is a need to advance our understanding of the effect of exposure to their combinations. Here we apply high-content microscopy imaging of cells stained with multiplexed dyes (Cell Painting) to profile the effects of Cetyltrimethylammonium bromide (CTAB), Bisphenol A (BPA), and Dibutyltin dilaurate (DBTDL) exposure on four human cell lines; both individually and in all combinations. We show that morphological features can...

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.

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...

Targeted sequencing of 252 genes based on their relevance in lymphoid malignancies

Silvia Bonfiglio, Lesley-Ann Sutton, Viktor Ljungström, Antonella Capasso, Tatjana Pandzic, Simone Weström, Hassan Foroughi Asl, Aron Skaftason, Anna Gellerbring, Anna Lyander, Francesca Gandini, Gianluca Gaidano, Livio Trentin, Lisa Bonello, Gianluigi Reda, Csaba Bodor, Niki Stravoyianni, Costantine S. Tam, Roberto Marasca, Francesco Forconi, Panayiotis Panayiotidis, Ingo Ringshausen, Ozren Jakšić, Alessandra Tedeschi, Anna Maria Frustaci … & Paolo Ghia
Dataset description Data consists of CRAM file from capture-based gene panel sequencing (Twist Bioscience) of 252 genes selected based on their relevance in lymphoid malignancies. The panel also included genome-wide backbone probes for copy-number analysis. The preprared libraries were then subsequenlty equenced in paired-end mode (2x150bp) on the Illumina NovaSeq 6000 (Illumina Inc.). BALSAMIC was used to analyze the FASTQ files and aligning them to reference genome. Trimmed reads were mapped to the reference genome...

COMMUNITY study

Charlotte Thålin, Sophia Hober, Mia Phillipson, Sara Mangsbo, Peter Nilsson & Sebastian Havervall
The COMMUNITY study is a longitudinal cohort study including 2149 healthcare workers and 118 COVID-19 patients.
Dataset includes:1. Serological data at baseline April-May 2020 and at four-month follow-up.
2. Self-reported symptoms compatible with COVID-19 since 1 January 2020, occupation, work location and exposure to patients infected with COVID-19 prior to blood sampling (healthcare workers).
3. Clinical data including co-morbidities, laboratory data, disease severity, on-going medications, demography (COVID-19 patients).

AbstractThe COMMUNITY study is a large longitudinal cohort study...

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...

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...

Single Cell Smart-Seq 3 RNA-Seq and Bulk Exome Seq from Breast Cancer Patients

Seong-Hwan Jun, Hosein Toosi, Jeff Mold, Camilla Engblom, Xinsong Chen, Ciara O’Flanagan, Michael Hagemann-Jensen, Rickard Sandberg, Johan Hartman, Samuel Aparicio, Andrew Roth & Jens Lagergren
Data Set Description
Single cell RNA sequencing (Samrt-Seq3) and Whole exome sequencing from multiple regions of individual tumors from Breast Cancer patients and also single cell RNA seq for two ovarian cancer cell lines.
The dataset contains raw sequencing data for various high-throughput molecular tests performed on two sample types: tumor samples from two breast cancer patients and cell lines derived from High-grade serous carcinoma Patients.

The breast cancer data comes from two patients: patient 1 (BCSA1)...

Single Cell Smart-Seq 3 RNA-Seq and Bulk Exome Seq from Breast Cancer Patients

Seong-Hwan Jun, Hosein Toosi, Jeff Mold, Camilla Engblom, Xinsong Chen, Ciara O’Flanagan, Michael Hagemann-Jensen, Rickard Sandberg, Johan Hartman, Samuel Aparicio, Andrew Roth & Jens Lagergren
Data Set Description
Single cell RNA sequencing (Samrt-Seq3) and Whole exome sequencing from multiple regions of individual tumors from Breast Cancer patients and also single cell RNA seq for two ovarian cancer cell lines.
The dataset contains raw sequencing data for various high-throughput molecular tests performed on two sample types: tumor samples from two breast cancer patients and cell lines derived from High-grade serous carcinoma Patients.

The breast cancer data comes from two patients: patient 1 (BCSA1)...

Data from: SweHLA: the high confidence HLA typing bio-resource drawn from 1 000 Swedish genomes

Jessika Nordin, Adam Ameur, Ulf Gyllensten & Jennifer R.S. Meadows
HLA allele frequency data from the 1000 Swedish individuals included in SweGen

Data and scripts for Mol Ecol article by Jahnke et al: Seascape genomics identify adaptive barriers correlated to tidal amplitude in the shore crab Carcinus maenas

Marlene Jahnke, Per-Olav Moksnes, Alan Le Moan, Gerrit Martens & Per R Jonsson
This repository includes data files and scripts used in the publication "Seascape genomics identify adaptive barriers correlated to tidal amplitude in the shore crab Carcinus maenas" published in Molecular Ecology in 2022.In this publication we assessed 12 sites in the native range of the European shore crab Carcinus maenas spanning >2000 km, and examined genetic structure and selection to tidal gradient using 24,000 Single Nucleotide Polymorphisms (SNPs) derived from 2b-RAD sequencing. Additionally, we performed biophysical...

Single base substitution and insertion/deletion mutational signatures in adult core binding factor acute myeloid leukemia

Rebeqa Gunnarsson, Minjun Yang, andrea Biloglav, Vladimir Lazarevic, Kajsa Paulsson & Bertil Johansson
Paired diagnostic and remission samples from 20 adults with core binding factor acute myeloid leukemia (AML), comprising ten with t(8;21)(q22;q22) [RUNX1::RUNX1T1] and ten with inv(16)(p13q22)/t(16;16)(p13;q22) [CBFB::MYH11] analyzed by whole genome sequencing are included in this data set. All patients had de novo AML and the cases were selected based on the availability of good quality DNA from both diagnosis and remission. The median age of the patients was 51.5 years (range 19-74 years) and the...

Single base substitution and insertion/deletion mutational signatures in adult core binding factor acute myeloid leukemia

Rebeqa Gunnarsson, Minjun Yang, andrea Biloglav, Vladimir Lazarevic, Kajsa Paulsson & Bertil Johansson
Paired diagnostic and remission samples from 20 adults with core binding factor acute myeloid leukemia (AML), comprising ten with t(8;21)(q22;q22) [RUNX1::RUNX1T1] and ten with inv(16)(p13q22)/t(16;16)(p13;q22) [CBFB::MYH11] analyzed by whole genome sequencing are included in this data set. All patients had de novo AML and the cases were selected based on the availability of good quality DNA from both diagnosis and remission. The median age of the patients was 51.5 years (range 19-74 years) and the...

Hyperthermia-induced in situ drug amorphization by superparamagnetic nanoparticles in oral dosage forms

Shaquib Rahman Ansari, Alexandra Teleki, Shno Asad, Nele-Johanna Hempel, Peter Svedlindh, Korbinian Lobmann & Christel AS Bergström
Superparamagnetic iron oxide nanoparticles (SPIONs) generate heat upon exposure to an alternating magnetic field (AMF) which has been studied for hyperthermia treatment and triggered drug release. This study introduces a novel application of magnetic hyperthermia to induce amorphization of a poorly aqueous soluble drug, celecoxib, in situ in tablets for oral administration. In situ amorphization can overcome the drug development hurdle of poor aqueous solubility by molecularly dispersing the drug in a polymeric network inside...

LNP drug delivery image data

Philip Harrison, Håkan Wieslander, Alan Sabirsh, Johan Karlsson, Victor Malmsjö, Andreas Hellender, Carolina Wählby & Ola Spjuth
Data to accompany the manuscript "Deep learnings models for lipid-nanoparticle-based drug delivery"
Abstract:Large-scale time-lapse microscopy experiments are useful to understand delivery and expression in RNA-based therapeutics. The resulting data has high dimensionality and high (but sparse) information content, making it challenging and costly to store and process. Early prediction of experimental outcome enables intelligent data management and decision making. We start from time-lapse data of HepG2 cells exposed to lipid-nanoparticles loaded with mRNA for expression of...

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...

Single cell RNA sequencing data from: Clonal competition within complex evolutionary hierarchies shapes AML over time.

Carl Sandén, Henrik Lilljebjörn, Christina Orsmark Pietras, Rasmus Henningsson, Karim H. Saba, Niklas Landberg, Hanna Thorsson, Sofia Von Palffy, Pablo Peña-Martinez, Carl Högberg, Marianne Rissler, David Gisselsson, Vladimir Lazarevic, Gunnar Juliusson, Helena Ågerstam & Thoas Fioretos
10x genomics single cell RNA sequencing data (fastq-files) from three samples representing one AML and two xenografted samples.

Data from: AML Display Increased CTCF Occupancy Associated to Aberrant Gene Expression and Transcription Factor Binding

Huthayfa Mujahed, Andreas Lennartsson & Soren Lehmann
RNA-seq, ChIP-seq and Methylation array data from fifteen Acute Myeloid Leukemia patients and five normal donors.

StratFreshDB v1.1

Moritz Buck
Stratified lakes and ponds that feature steep oxygen gradients are known to be significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the resident microbial communities, especially in the oxygen-depleted hypolimnetic compartments are poorly known. In this paper, we present a comprehensive metagenome dataset including shotgun metagenomes from 29 stratified lakes and 12 ponds mainly located in the boreal and subarctic regions but also including one reservoir...

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...

Data from: Transcriptomic analysis reveals pro-inflammatory signatures associated with acute myeloid leukemia progression

Linda Holmfeldt & Svea Stratmann
Data Set Description
These data are collected from a total of 70 participants (47 adult; 23 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. (https://doi.org/10.1182/bloodadvances.2021004962). The Stratmann et. al. study is currently pre-published here: https://ashpublications.org/bloodadvances/article/doi/10.1182/bloodadvances.2021004962/477210/Transcriptomic-analysis-reveals-pro-inflammatory Please note that separate applications are necessary for the adult and pediatric...

Data from paper: Palmdelphin Regulates Nuclear Resilience to Mechanical Stress in the Endothelium

Lena Claesson-Welsh & Miguel Sainz Jaspeado
Raw data from bulk RNA-Seq on endothelial cell cultures grown under static or laminar flow conditions after silencing Palmdelphin or not.
Paper abstract: Background: Palmdelphin (PALMD), a protein of unknown function, belongs to the family of Paralemmin proteins implicated in cytoskeletal regulation. Single nucleotide polymorphisms (SNPs) in the PALMD locus, which reduce its expression, are strong risk factors for development of calcific aortic valve stenosis (CAVS) and for severity of the disease.Methods: Public database screening and...

Consiglio et al 2020 Cell The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19

Petter Brodin
Publication: "The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19".
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.

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...

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...

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