175 Works

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)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.

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.

raw_data_SMCT_FCS.tar.gz

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.

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...

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...

Gold Stamp IDs to SRA IDs convertion of the metagenomes of GEMs

Moritz Buck
A small simple JSON-file containing the mapping from Gold Stamp IDs from the IMG/JGI database to the SRA IDs useable by fastq-dump to download the corresponding metagenomes from NCBI. The GoldIDs are the ones from the Supplemental Table 1 from Nayfach, S., Roux, S., Seshadri, R. et al. A genomic catalog of Earth’s microbiomes. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0718-6, that have been submited to the Short Read Archive. The code used to generate this mapping is...

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...

Test dataset from: GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

Verena Kutschera, Marcin Kierczak, Tom van der Valk, Johanna von Seth, Nicolas Dussex, Edana Lord, Marianne Dehasque, David W. G. Stanton, Payam Emami Khoonsari, Björn Nystedt, Love Dalén & David Díez del molino
This item contains a test dataset based on Sumatran rhinoceros (Dicerorhinus sumatrensis) whole-genome re-sequencing data that we publish along with the GenErode pipeline (https://github.com/NBISweden/GenErode; Kutschera et al. 2022) and that we reduced in size so that users have the possibility to get familiar with the pipeline before analyzing their own genome-wide datasets. We extracted scaffold ‘Sc9M7eS_2_HRSCAF_41’ of size 40,842,778 bp from the Sumatran rhinoceros genome assembly (Dicerorhinus sumatrensis harrissoni; GenBank accession number GCA_014189135.1) to be...

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...

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...

SPARC single-cell protein data

Johan Reimegård
This data set contains protein measurements from single cell and 100 cells from early human neural differentiation cells. Cells were harvested at time points 0 h, 24 h and 48 h.
Protein data measurements were carried out using PEA and quantitative values on protein concentrations were measures using qPCR. Following the completion of the qPCR run we visually inspected the amplification curves. Samples showing evidence of failed or poor amplification reactions were excluded from further analysis....

Duplex sequencing uncovers recurrent low-frequency cancer-associated mutations in KMT2A-rearranged infant acute leukemia

Mattias Pilheden & Anna Hagström Andersson
This dataset includes Duplex sequencing and targeted next generation sequencing (NGS) of 20 Infants and 7 Children with acute lymphoblastic leukmia. All patients had an underlying rearrangement of the KMT2A gene, either KMT2A::MLLT3 (n=5), KMT2A::AFF1 (n=12), KMT2A::MLLT1 (n=8) or KMT2A::MLLT10 (n=2). The median age of the cohort was 7 months. Diagnostic sample from peripheral blod (n=11) or bone marrow (n=16) underwent the duplex sequencing library preparation as described in https://doi.org/10.1073/pnas.1208715109 and sequenced on the NextSeq...

Data: Gene expression profile in peripheral B-lymphocytes and sera of individuals with fibromyalgia

Joakim Klar
Overview Fibromyalgia (FM) is an idiopathic chronic disease characterized by widespread musculoskeletal pain, hyperalgesia and allodynia, often accompanied by fatigue, cognitive dysfunction and other symptoms. We investigated the gene expression profile in peripheral B-cells in FM patients and healthy matched control individuals.
Summary The uploaded data consist of count table and sample information and can be used for gene expression analysis of patients and controls.
Generation of Data A total of 100 ng...

SH information from UNITE databases

Jeanette Tångrot
The data is the result of querying the PlutoF API (https://plutof.docs.apiary.io, Abarenkov et al 2010) with all sequence names in the UNITE general FASTA release (https://doi.org/10.15156/BIO/786368; Abarenkov et al. 2020, https://doi.org/10.15156/BIO/1280049; Abarenkov et al. 2021), in order to find the sequence hypothesis (SH) at level 1.5, version 8, for each sequence, resulting in a sequence-to-SH matching file (*.seq2SH.tsv). For each SH, the complete taxonomy is extracted from PlutoF by querying the PlutoF API, and stored...

WGS for patient specific MRD in pediatric ALL

Cecilia Arthur, Fatemah Rezayee, Nina Mogensen, Leonie Saft, Richard Rosenquist Brandell, Magnus Nordenskjöld, Arja Harila-Saari, Emma Tham & Gisela Barbany
Data from a study of six children with acute lymphoblastic leukemia (four patients with precursor B-cell ALL (Acute lymphoblastic leukemia) and two patients with T-cell ALL). None had stratifying genetics or central nervous system involvement. The study was approved by the Ethical Review Board at Stockholm County and written informed consent was obtained from the patients’ guardians.
The data consits of BAM-files from whole-genome sequencing (WGS) of diagnostic bone marrow samples (30X coverage on...

Chromium Next GEM Single Cell 3’ RNA-sequencing of tumor cell line co-cultured with PBMC and treated with trifluridine or DMSO control

Claes Andersson & Tove Selvin
Chromium Next GEM Single Cell 3’ RNA-sequencing.
HCT116 were seeded in 6-well Nunc plates (50,000 cells/3mL/well) and precultured for 24 h before PBMCs were added at a 1:8 ratio. Co-cultures were treated with DMSO vehicle (0.1%) or FTD (3mM) for 12 h or 72 h. MACS Dead Cell Removal Kit (Miltenyi Biotec, Gladbach, DEU) was performed according to the manufacturer’s instructions on cells treated for 72 h to increase the viability of the samples...

Single-cell gene expression count data for trifluridine treated co-culture of tumor cell line with PBMC

Claes Andersson & Tove Selvin
Gene expression (counts) scRNA-seq of co-cultured cancer- and immune cells treated with trifluridine and DMSO control assayed at two time-points (12h and 72h).
HCT116 were seeded in 6-well Nunc plates (50,000 cells/3mL/well) and precultured for 24 h before PBMCs were added at a 1:8 ratio. Co-cultures were treated with DMSO vehicle (0.1%) or FTD (3mM) for 12 h or 72 h. MACS Dead Cell Removal Kit (Miltenyi Biotec, Gladbach, DEU) was performed according to...

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