88 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...

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...

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...

COMMUNITY study

Charlotte Thålin, Sophia Hober, Mia Phillipson, Sara Mangsbo, Peter Nilsson & Sebastian Havervall
The COMMUNITY study 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 four-month follow-up.
2. Self-reported symptoms compatible with COVID-19 since 1 January 2020, occupation, work location and exposure to patients infected with COVID-19 prior to blood sampling (healthcare workers).
3. Clinical data including co-morbidities, laboratory data, disease severity, on-going medications, demography (COVID-19 patients).

AbstractThe COMMUNITY study is a large longitudinal cohort study...

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)...

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...

CSAW-M: An Ordinal Classification Dataset for Benchmarking Mammographic Masking of Cancer

Moein Sorkhei, Yue Liu, Hossein Azizpour, Edward Azavedo, Karin Dembrower, Dimitra Ntoula, Anthanasios Zouzos, Fredrik Strand & Kevin Smith
Welcome to the the CSAW-M dataset homepage
This page includes the files and metadata related to the CSAW-M, a curated dataset of mammograms with expert assessments of the masking of cancer. CSAW-M is collected from over 10,000 individuals and annotated with potential masking. In contrast to the previous approaches which measure breast image density as a proxy, our dataset directly provides annotations of masking potential assessments from five specialists. We trained deep learning models on CSAW-M...

Data from: Transcriptomic analysis reveals pro-inflammatory signatures associated with acute myeloid leukemia progression

Linda Holmfeldt & Svea Stratmann
Data Set Description
These data are collected from a total of 70 participants (47 adult; 23 pediatric), all of which had relapsed or primary resistant acute myeloid leukemia. The data, which here are separated into an adult and a pediatric dataset, were generated as part of a study by Stratmann et. al. (https://doi.org/10.1182/bloodadvances.2021004962). The Stratmann et. al. study is currently pre-published here: https://ashpublications.org/bloodadvances/article/doi/10.1182/bloodadvances.2021004962/477210/Transcriptomic-analysis-reveals-pro-inflammatory Please note that separate applications are necessary for the adult and pediatric...

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...

Registration Year

  • 2021
    88

Resource Types

  • Dataset
    88