232 Works

Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH (Dataset 1: miFISH chr2 Replicate 1)

Ana Faustino Mota, Maud Schweitzer & Magda Bienko
We designed 16 probes targeting 16 consecutive loci on chromosome 2 using iFISH4U. The 16 probes targetting different loci are spaced with 3 or 20 Mb in order to study relatively small genomic distances and compare them with larger distances. Furthermore, 10 loci are made of a combination of two colours alternating within the locus and 6 loci have only one colour. Replicate 1

Experiment Imaging Method: epifluorescence microscopy
Protocol Name: iFISH protocol

Each dataset consists of multiple...

SBDI Sativa curated 16S GTDB database

Daniel Lundin & Anders Andersson
The data in this repository is the result of vetting 16S sequences from the GTDB database release R06-RS202 (https://gtdb.ecogenomic.org/; Parks et al. 2018) with the Sativa program (Kozlov et al. 2016).

Files for the DADA2 (Callahan et al. 2016) methods `assignTaxonomy` and `addSpecies` are available.
Both files are gzipped fasta files with 16S sequences, the assignTaxonomy associated with taxonomy hierarchies from domain to genus whereas the addSpecies file have sequence identities and species names.

Taxonomical annotation of 16S...

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...

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...

SBDI Sativa curated 16S GTDB database

Daniel Lundin & Anders Andersson
The data in this repository is the result of vetting 16S sequences from the GTDB database release R06-RS202 (https://gtdb.ecogenomic.org/; Parks et al. 2018) with the Sativa program (Kozlov et al. 2016).

Files for the DADA2 (Callahan et al. 2016) methods `assignTaxonomy` and `addSpecies` are available: gtdb-sbdi-sativa.r06rs202.assignTaxonomy.fna.gz and gtdb-sbdi-sativa.r06rs202.addSpecies.fna.gz.
There is also a fasta file with the original GTDB sequence names: gtdb-sbdi-sativa.r06rs202.fna.gz
All three files are gzipped fasta files with 16S sequences, the assignTaxonomy associated with taxonomy hierarchies from...

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 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...

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...

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.

Single base substitution mutational signatures in pediatric acute myeloid leukemia based on whole genome sequencing

Rebeqa Gunnarsson, Minjun Yang, Linda Olsson Arvidsson, andrea Biloglav, Mikael Behrendtz, Anders Castor, Kajsa Paulsson & Bertil Johansson
This dataset includes whole genome sequencing (WGS) data of 20 diagnostic, and 20 remission samples from 20 children/adolescents with acute myeloid leukemia (AML), treated at the Departments of Pediatrics at Lund and Linköping University Hospitals between 1994 and 2016. The median age of the patients was 8 years (range 0-17 years) and the female/male ratio was 1:1. DNA was extracted from diagnostic bone marrow (BM; n = 17)/peripheral blood (PB; n = 3) samples, remission...

Modelling of Large Protein Complexes

Patrick Bryant & Arne Elofsson
AlphaFold and AlphaFold-multimer can predict the structure of single- and multiple chain proteins with very high accuracy. However, predicting protein complexes with more than a handful of chains is still unfeasible, as the accuracy rapidly decreases with the number of chains and the protein size is limited by the memory on a GPU. Nevertheless, it might be possible to predict the structure of large complexes starting from predictions of subcomponents. Here, we take a graph...

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...

Swedish National Seismic Network

The Swedish National Seismic Network (SNSN) started with the installation of a Wiechert seismograph in Uppsala in 1904. Since 1998 the SNSN is a part of the Department of Earth Sciences at Uppsala University. The SNSN operates the only permanent, earthquake focused seismic network in Sweden and is responsible for detecting and recording earthquakes in Sweden. Near real-time automatic event detection has been an integral part of SNSN operations since 2000 and continuous 100 Hz...

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

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...

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...

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.

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