53 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...

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.

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...

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...

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.

Fluent Python nuggets. A brief presentation.

Per Kraulis
Some nuggets of Python coding wisdom out of the book Fluent Python by Lucian Ramalho. A light-weight presentation.

Life Science Data Management lecture

Niclas Jareborg
Video recording of a general lecture about Data Management practices for Life Science in three parts, and a pdf with the slides.
Note! The sound for the movie in part 3 doesn't work. Please go to the Youtube clip and watch it: https://www.youtube.com/watch?v=N2zK3sAtr-4.

Life Science Data Management lecture

Niclas Jareborg
Video recording of a general lecture about Data Management practices for Life Science in three parts, and a pdf with the slides.
Note! The sound for the movie in part 3 doesn't work. Please go to the Youtube clip and watch it: https://www.youtube.com/watch?v=N2zK3sAtr-4.

Genome Informatics 2020 --- Poster

Moritz Buck
Poster presented at Genome Informatics 2020. Describing mOTUpan.py from mOTUlizer (https://github.com/moritzbuck/mOTUlizer).
Careful, probability computation have changed somewhat since this poster!

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...

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...

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...

5PSeq analysis conecting translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae

Vicent Pelechano & Alisa Alekseenko
Supplementary information for the manuscript: A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae. Olga Rodríguez-Galán, Juan J García-Gómez, Iván V Rosado, Wu Wei, Alfonso Méndez-Godoy, Benjamin Pillet, Alisa Alekseenko, Lars M Steinmetz, Vicent Pelechano, Dieter Kressler, Jesús de la Cruz, Nucleic Acids Research, , gkaa1200, https://doi.org/10.1093/nar/gkaa1200
Here we provide browsable metagene analysis for 5´P mRNA degradation profiles.Raw and processed sequencing data are deposited at Gene Expression Omnibus...

Data from: A systems biology approach identifies B cell maturation antigen (BCMA) as biomarker reflecting oral vaccine induced IgA antibody responses in humans

Lynda Mottram, Anna Lundgren, & Susannah Leach
In this study, RNA-Seq was performed on peripheral blood mononuclear cells (PBMCs) isolated from six volunteers of a oral cholera Dukoral® vaccine study performed by Mottram et al., 2020.(10.1016/j.vaccine.2019.10.050).
The raw FASQ and indexed aligned BAM files described here were taken from four strong and two non IgA antibody responders of this Dukoral® vaccine study and are part of another study described by Mottram et al (2021) (Frontiers in Immunology, accepted for publication).
Total...

Improved computational analysis of ribosome dynamics from 5’P degradome data using fivepeseq

Vicent Pelechano, Lilit Nersisyan & Maria Ropat
Supplementary information for manuscript: "Improved computational analysis of ribosome dynamics from 5’P degradome data using fivepeseq" from Lilit Nersisyan, Maria Ropat and Vicent Pelechano (2020)
Dataset updated to fivepseq version1.0b6

5'P mRNA degradome datasets analyzed with fivepseq. (http://pelechanolab.com/software/fivepseq/). Raw Saccharomyces cerevisiae data is available from GEO under accession code GSE91064 and for Arabidopsis thaliana under accessions GSE72505 and GSE77549.

ELIXIR Proteomics Community - Connection with nf-core

Phil Ewels
A joint effort on the standardization of analytics workflows.
Phil Ewels (@ewels) will give a talk followed by discussion for one of the ELIXIR Proteomics Community regular monthly meetings, to speak about nf-core and how the two communities can work together.
You can catch up with the YouTube video at https://youtu.be/vxDv_hVkycM.

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...

SMCT-FCS data from DNA surface exploration and operator bypassing during target search

Emil Marklund, Brad Van Oosten, , Elias Amselem, Kalle Kipper, Anton Sabantsev, Andrew Emmerich, Daniel Globisch, Xuan Zheng, Laura Lehmann, Otto Berg, Magnus Johansson, Johan Elf & Sebastian Deindl
Single-molecule confocal laser tracking combined with fluorescence correlation spectroscopy dataset of lac repressor molecules sliding on flow-stretched DNA, as in Marklund et al., Nature, 2020.

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