88 Works

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

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...

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 used in exercises in course Introduction to Data Management Practices

Yvonne Kallberg, Elin Kronander, Niclas Jareborg, Markus Englund &
This record contains the data files used in exercises in the NBIS course "Introduction to Data Management Practices".

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...

DNA methylation signatures predict cytogenetic subtype and outcome in pediatric acute myeloid leukemia (AML)

Olga Krali, Josefine Palle, Christofer Bäcklin, Jonas Abrahamsson, Ulrika Norén-Nyström, Henrik Hasle, Kirsi Jahnukainen, Ólafur Gísli Jónsson, Randi Hovland, Birgitte Lausen, Rolf Larsson, Lars Palmqvist, Anna Staffas, Bernward Zeller & Jessica Nordlund
This dataset contains genome-wide DNA methylation data generated from 142 pediatric acute myeloid leukemia (AML) samples originating from bone marrow or peripheral blood samples taken at AML diagnosis (N=123) or relapse (N=19). Further details regarding the samples are available in Supplementary Table S1 from Krali and Palle et. al., 2021 (https://doi.org/10.3390/genes12060895).Genome-wide DNA methylation was analyzed at the SNP&SEQ Technology Platform, SciLifeLab, National Genomics Infrastructure Uppsala, Sweden. 200ng of bisulfite converted DNA was amplified, fragmented and...

DNA methylation signatures predict cytogenetic subtype and outcome in pediatric acute myeloid leukemia (AML)

Olga Krali, Josefine Palle, Christofer Bäcklin, Jonas Abrahamsson, Ulrika Norén-Nyström, Henrik Hasle, Kirsi Jahnukainen, Ólafur Gísli Jónsson, Randi Hovland, Birgitte Lausen, Rolf Larsson, Lars Palmqvist, Anna Staffas, Bernward Zeller & Jessica Nordlund
This dataset contains genome-wide DNA methylation data generated from 142 pediatric acute myeloid leukemia (AML) samples originating from bone marrow or peripheral blood samples taken at AML diagnosis (N=123) or relapse (N=19). Further details regarding the samples are available in Supplementary Table S1 from Krali and Palle et. al., 2021 (https://doi.org/10.3390/genes12060895).Genome-wide DNA methylation was analyzed at the SNP&SEQ Technology Platform, SciLifeLab, National Genomics Infrastructure Uppsala, Sweden. 200ng of bisulfite converted DNA was amplified, fragmented and...

Dataset of SARS-CoV-2 in wastewater in Umeå, Sweden

Maja Malmberg, Mette Myrmel &
This is a metadata record for a continuously updated dataset of SARS-CoV-2 RNA data in wastewater in Umeå, Sweden.The dataset is part of a research study led by associate professor Maja Malmberg (SLU, Swedish University of Agricultural Sciences) and her research group in collaboration with associate professor Mette Myrmel at the Norwegian University of Life Sciences.
The amount of SARS-CoV-2 virus is measured in wastewater from the wastewater treatment facility in Umeå. The research group is...

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...

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...

CODE dataset

Antonio H. Ribeiro, Manoel Horta Ribeiro, Gabriela M. Paixão, Derick M. Oliveira, Paulo R. Gomes, Jéssica A. Canazart, Milton P. Ferreira, Carl R. Andersson, Peter W. Macfarlane, Wagner Meira Jr., Thomas B. Schön & Antonio Luiz P. Ribeiro
Dataset with annotated 12-lead ECG records. The exams were taken in 811 counties in the state of Minas Gerais/Brazil by the Telehealth Network of Minas Gerais (TNMG) between 2010 and 2016. And organized by the CODE (Clinical outcomes in digital electrocardiography) group.
Requesting access
Researchers affiliated to educational or research institutions might make requests to access this data dataset. Requests will be analyzed on an individual basis and should contain: Name of PI and host organisation; Contact...

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...

Data and most relevant results for the FoldDock project

Patrick Bryant, Gabriele Pozzati & Arne Elofsson
Data and main results for the study "Improved prediction of protein-protein interactions using AlphaFold2 and extended multiple-sequence alignments."
Contained datasets consist of:1 - 219 heterodimers from dockground benchmark 4 dataset 2 - 1503 heterodimeric structures from a recent study (Green, A. G. et al. Nat. Commun. 12, 1–12 (2021))3 - 7 heterodimeric complexes from CASP144 - 8 novel heterodimeric complexes deposited in the PDB database after 15 June 2021
For each one of the mentioned datasets it...

Registration Year

  • 2021
    88

Resource Types

  • Dataset
    88