245 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.

NBIS DOI collection

This collection contains permanent identifiers (issued by NBIS before April 2020) to data sets generated by Life Science researchers active in Sweden and for which no other suitable public repository was available.
NBIS is a distributed national research infrastructure supported by the Swedish Research Council (Vetenskapsrådet) providing bioinformatics support to life science researchers in Sweden.

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...

Introductory presentation of Sphinx and Linters in Python

Linus Östberg
A basic introduction to the use of Sphinx and a few different Python linters.

Introductory presentation of Sphinx and Linters in Python

Linus Östberg
A basic introduction to the use of Sphinx and a few different Python linters.

COVID-19 Data Portal - data sharing for accelerating research

Arnold Kochari
Slides presented at the 'FAIR principles in life science research practice' event, organised by ELIXIR-SE/NL and SciLifeLab Data Centre on December 9, 2021.

The Swedish COVID-19 Data Portal (https://covid19dataportal.se/) was launched in June 2020 to support the open sharing and reuse of data related to COVID-19 and SARS-CoV-2 from Swedish research institutes. Open data sharing is important for accelerating research, but being shared openly does not necessarily mean that the data is good quality or useful....

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...

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...

Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH (Dataset 9: iFISH chr10 spotting Replicate 2)

Ana Faustino Mota, Maud Schweitzer & Magda Bienko
We designed 13 probes targeting 13 consecutive loci on chromosome 10 using iFISH4U. The 23 loci are spaced with 10 Mb. There are 2 probes with AF488 dye, 2 probes with AT542, 3 probes with AF594, 2 probes with AT647N, 2 probes with AF700 and 2 probes with AF790. Replicate 2
Experiment Imaging Method: epifluorescence microscopy
Protocol Name: iFISH protocol

Each dataset consists of multiple fields of view (FOVs) that were acquired with seven different dyes (AF488 labeled...

Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH (Dataset 9: iFISH chr10 spotting Replicate 2)

Ana Faustino Mota, Maud Schweitzer & Magda Bienko
We designed 13 probes targeting 13 consecutive loci on chromosome 10 using iFISH4U. The 23 loci are spaced with 10 Mb. There are 2 probes with AF488 dye, 2 probes with AT542, 3 probes with AF594, 2 probes with AT647N, 2 probes with AF700 and 2 probes with AF790. Replicate 2
Experiment Imaging Method: epifluorescence microscopy
Protocol Name: iFISH protocol

Each dataset consists of multiple fields of view (FOVs) that were acquired with seven different dyes (AF488 labeled...

Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH (Dataset 8: iFISH chr10 spotting Replicate 1)

Ana Faustino Mota, Maud Schweitzer & Magda Bienko
We designed 13 probes targeting 13 consecutive loci on chromosome 10 using iFISH4U. The 23 loci are spaced with 10 Mb. There are 2 probes with AF488 dye, 2 probes with AT542, 3 probes with AF594, 2 probes with AT647N, 2 probes with AF700 and 2 probes with AF790. Replicate 1
Experiment Imaging Method: epifluorescence microscopy
Protocol Name: iFISH protocol

Each dataset consists of multiple fields of view (FOVs) that were acquired with seven different dyes (AF488 labeled...

Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH (Dataset 4: miFISH with one dual-color probe AT647N-AT542 and two single-color probes AF594 and AF488)

Ana Faustino Mota, Maud Schweitzer & Magda Bienko
We performed a single colour experiment where one probe with alternated colours (AT542-AT647N) was tested together with other two probes in different colours located in distinct genomic sites. There are 1 probe with AF488 dye, 1 probe with AT542, 1 probe with AF594 and 1 probe with AT647N.
Experiment Imaging Method: epifluorescence microscopy
Protocol Name: iFISH protocol

Each dataset consists of multiple fields of view (FOVs) that were acquired with seven different dyes (AF488 labeled as ‘a488’; AT542...

Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH (Dataset 5: iFISH chr1 spotting Replicate 1)

Ana Faustino Mota, Maud Schweitzer & Magda Bienko
We designed 23 probes targeting 23 consecutive loci on chromosome 1 using iFISH4U. The 23 loci are spaced with 10 Mb. There are 3 probes with AF488 dye, 4 probes with AT542, 4 probes with AF594, 4 probes with AT647N, 4 probes with AF700 and 4 probes with AF790. Replicate 1

Experiment Imaging Method: epifluorescence microscopy
Protocol Name: iFISH protocol

Each dataset consists of multiple fields of view (FOVs) that were acquired with seven different dyes (AF488...

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