182 Works

Distinct developmental pathways from blood monocytes generate human lung macrophage diversity

Tim Willinger & Elza Evren
RNA-sequencing data sets(1) Single-cell RNA-sequencing data of human lung myeloid cells from MISTRG mice on day 21 post-transplantation with human CD34+ cells (2) Single-cell RNA-sequencing data of human lung myeloid cells from MISTRG mice on day 36 post-transplantation with human CD34+ cells (3) Bulk RNA-sequencing data of human intravascular monocytes, intravascular macrophages, and extravascular macrophages from the lungs of MISTRG mice engrafted with human CD34+ cells
Data collection methodsSee Resource DOI

Publication abstractThe study of human macrophages...

StratFreshDB v1.0

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...

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...

GHG feature profiling with multiple definitions

Wenjing Kang, Bastian Fromm, Inna Biryukova & Marc Friedländer
This is the Supplemental Data 13 of the MapToCleave study.
This dataset is related to Figure 6E. The GHG feature is profiled based on the different definitions that are described in the method section “Identifying the presence of the GHG feature using different definitions”. The file “GHG_feature_MapToCleave.txt” shows the presence of the GHG features in the MapToCleave processed and unprocessed miRNA precursors. The file “GHG_feature_MirGeneDB.txt” shows the presence of the GHG features in MirGeneDB human...

Data from: RNA Sequencing Provides Novel Insights Into the Transcriptome of Aldosterone Producing Adenomas

Tobias Åkerström, Per Hellman & Peyman Björklund
RNA-Seq data from fifteen aldosterone producing adenomas. Whole Genome Sequencing data from two aldosterone producing adenomas and one normal peripheral blood sample.

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...

Local temporal Rac1-GTP nadirs and peaks restrict cell protrusions and retractions

Jianjiang Hu, Xiaowei Gong & Staffan Strömblad
Dataset used in the paper "Local temporal Rac1-GTP nadirs and peaks restrict cell protrusions and retractions".
The GTPase4.rar file contains the raw confocal images of HT1080 cell line stably expressing RhoA-2G or Rac-2G biosensors seeded on 6.9kPa polyacrylamid gel. Channel 1 and 2 are the FRET signals (excite 457nm, emission 482/35 nm and 525/50 nm). Channel 3 is the red fluorescent beads for the traction force calculation (by comparing to the corresponding cell free image file...

Local temporal Rac1-GTP nadirs and peaks restrict cell protrusions and retractions

Jianjiang Hu, Xiaowei Gong & Staffan Strömblad
Dataset used in the paper "Local temporal Rac1-GTP nadirs and peaks restrict cell protrusions and retractions".
The GTPase4.rar file contains the raw confocal images of HT1080 cell line stably expressing RhoA-2G or Rac-2G biosensors seeded on 6.9kPa polyacrylamid gel. Channel 1 and 2 are the FRET signals (excite 457nm, emission 482/35 nm and 525/50 nm). Channel 3 is the red fluorescent beads for the traction force calculation (by comparing to the corresponding cell free image file...

Genomic characterization of the barnacle Balanus improvisus reveals extreme nucleotide diversity in coding regions

Magnus Alm Rosenblad & Björn Nystedt
Pilot short-read genome assembly of one single adult barnacle, Balanus improvisus (=Amphibalanus imrpovisus), used to estimate genome size and heterocygosity. Bi01.clean.fa.gz is the final assembly with contaminations etc removed.
Alm Rosenblad et al., Marine Biotechnology 2021

Abstract Barnacles are key marine crustaceans in several habitats and they constitute a common practical problem by causing biofouling on man-made marine constructions and ships. Despite causing considerable ecological and economic impacts, there is a surprising void of basic genomic...

Genomic characterization of the barnacle Balanus improvisus reveals extreme nucleotide diversity in coding regions

Magnus Alm Rosenblad & Björn Nystedt
Pilot short-read genome assembly of one single adult barnacle, Balanus improvisus (=Amphibalanus imrpovisus), used to estimate genome size and heterocygosity. Bi01.clean.fa.gz is the final assembly with contaminations etc removed.
Alm Rosenblad et al., Marine Biotechnology 2021

Abstract Barnacles are key marine crustaceans in several habitats and they constitute a common practical problem by causing biofouling on man-made marine constructions and ships. Despite causing considerable ecological and economic impacts, there is a surprising void of basic genomic...

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...

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...

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...

Dataset of SARS-CoV-2 wastewater data from 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 Älvkarleby, 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 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 Älvkarleby, 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...

Association of CSF proteins with tau and amyloid β levels in asymptomatic 70-year-olds_Protein data

Julia Remnestål
A spread sheet with participant information on the concentration of Alzheimer's disease CSF markers (abeta42, t-tau and p-tau) as well as levels of brain-enriched proteins. The brain-enriched proteins are denoted by HGNC ID and antibody name.
This spreadsheet is connected to the manuscript Association of CSF proteins with tau and amyloid β levels in asymptomatic 70-year-olds published in Alzheimer's Research & Therapy in March 2021.
AbstractIncreased knowledge of the evolution of molecular changes in neurodegenerative disorders such...

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...

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...

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