127 Works

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...

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...

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...

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...

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...

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...

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  • 2021
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