230 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)
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.

Data from: Whole genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes

Sharadha Sakthikumar, Ananya Roy, Lulu Haseeb, Mats E. Pettersson, Elisabeth Sundström, Voichita D. Marinescu, Kerstin Lindblad-Toh & Karin Forsberg Nilsson
Data file associated with SweGBM-1 cohort WGS. A tab-delimited file containing the mutations and variant allele fraction of the cohort. The data file can be made available after applying for access, and agreeing to the terms and conditions for use.

Data from: De novo assembly of two Swedish genomes reveals missing segments from the human GRCh38 reference and improves variant calling of population-scale sequencing data

Adam Ameur & Ulf Gyllensten
De novo assembly of two individuals from the SweGen dataset

Random forest models for gene expression experiments in Transformational Machine Learning

Ivan Olier, Oghenejokpeme Orhobor, Tirtharaj Dash, Andy Davis, Larisa N. Soldatova, Joaquin Vanschoren & Ross King
Almost all machine learning (ML) is based on representing examples using intrinsic features. When there are multiple related ML problems (tasks), it is possible to transform these features into extrinsic features by first training ML models on other tasks and letting them each make predictions for each example of the new task, yielding a novel representation.
We call this transformational ML (TML). TML is very closely related to, and synergistic with, transfer learning, multi-task learning,...

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.

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!

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...

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...

Thermal Proteome Profiling dataset from Hazara virus infected SW13 cells treated with DMSO or antiviral inhibitor 20 µM TH6744.

Marjo Puumalainen, Marianna Tampere & Rozbeh Jafari
Article: S3 Dataset from a publication "Tampere, M.; Pettke, A.; Salata, C.; Wallner, O.; Koolmeister, T.; Cazares-Körner, A.; Visnes, T.; Hesselman, M.C.; Kunold, E.; Wiita, E.; Kalderén, C.; Lightowler, M.; Jemth, A.-S.; Lehtiö, J.; Rosenquist, Å.; Warpman-Berglund, U.; Helleday, T.; Mirazimi, A.; Jafari, R.; Puumalainen, M.-R. Novel Broad-Spectrum Antiviral Inhibitors Targeting Host Factors Essential for Replication of Pathogenic RNA Viruses. Viruses 2020, 12, 1423."
Abstract: Recent RNA virus outbreaks such as Severe acute respiratory syndrome...

Thermal Proteome Profiling dataset from Hazara virus infected SW13 cells treated with DMSO or antiviral inhibitor 20 µM TH6744.

Marjo Puumalainen, Marianna Tampere & Rozbeh Jafari
Article: S3 Dataset from a publication "Tampere, M.; Pettke, A.; Salata, C.; Wallner, O.; Koolmeister, T.; Cazares-Körner, A.; Visnes, T.; Hesselman, M.C.; Kunold, E.; Wiita, E.; Kalderén, C.; Lightowler, M.; Jemth, A.-S.; Lehtiö, J.; Rosenquist, Å.; Warpman-Berglund, U.; Helleday, T.; Mirazimi, A.; Jafari, R.; Puumalainen, M.-R. Novel Broad-Spectrum Antiviral Inhibitors Targeting Host Factors Essential for Replication of Pathogenic RNA Viruses. Viruses 2020, 12, 1423."
Abstract: Recent RNA virus outbreaks such as Severe acute respiratory syndrome...

Swedish National study on Aging and Care in Kungsholmen (SNAC-K) COVID-19 Study

Laura Fratiglioni, Giorgi Beridze & Amaia Calderón-Larrañaga
Abstract These data are collected from 1428 older adults aged 60 and above. The project is embedded in the ongoing Swedish National Study on Aging and Care in Kungsholmen (SNAC-K), a population-based study with regular health assessments since 2001. https://www.snac-k.se/
The SNAC-K COVID-19 study aims to: 1) Estimate the short-term collateral damage on older adults’ health during the first months of the COVID-19 outbreak; 2) Detect the long-term collateral repercussions on older adults health up to...

Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2

Niclas Roxhed, Annika Bendes, Matilda Dale, Cecilia Mattsson, Leo Hanke, Tea Dodig-Crnkovic, Christian Murray, Birthe Meineke, Simon Elsässer, Juni Andrell, Sebastian Haverall, Charlotte Thålin, Carina Eklund, Joakim Dillner, Olof Beck, Cecilia Engel Thomas, Gerald M. McInerney, Mun-Gwan Hong, Ben Murrell, Claudia Fredolini & Jochen Schwenk
Dried blood spot (DBS) samples were collected during spring of 2020 from random and undiagnosed individuals in Stockholm, Sweden.
Receiving DBS from 878 participants, we applied multiplexed serology assays to determine IgG and IgM levels against several versions of SARS-CoV-2 proteins (S, RBD, N).
The data reports anonymised an normalised "relative antibody titers" obtained in the eluates of the DBS samples. The data can be made available for validation purposes and upon reasonable request.
A reasonable...

Dataset of SARS-CoV-2 wastewater data from Östhammar, Sweden

Anna Székely & Nahla Mohamed
This is a metadata record for a continuously updated dataset of SARS-CoV-2 RNA data in wastewater in Östhammar, 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 Östhammar, Sweden

Anna Székely & Nahla Mohamed
This is a metadata record for a continuously updated dataset of SARS-CoV-2 RNA data in wastewater in Östhammar, 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 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...

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

Maja Malmberg, Mette Myrmel &
This is a metadata record for a continuously updated dataset of SARS-CoV-2 RNA data in wastewater in Örebro, 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 Örebro. The research group...

SciLifeLab Data Repository Launch

Johan Rung, Megan Hardeman, Vicent Pelechano, Jonne Rietdijk, Mikael Sellin & Wolmar Nyberg Åkerström
Presentations given at the digital launch event of the SciLifeLab Data Repository on May 7th 2021. The event was organized by SciLifeLab Data Centre. This event was recorded, a link to the recording is provided in the 'references' field of this item.
Event agenda: Introduction - Johan Rung (SciLifeLab Data Centre)Storing, sharing, and citing your data with SciLifeLab's Figshare - Megan Hardeman (Figshare)User perspectives - Vicent Pelechano (Karolinska Institutet)- Jonne Rietdijk (Uppsala University- Mikael Sellin (Uppsala...

Conceptualising the Mastery Rubric for Bioinformatics - Applications to training & professional development

Jessica Lindvall, Teresa Attwood, Allegra Via & Rochelle Tractenberg
Target audience: Life Science community
Learning Outcomes: By the end of the presentation you will be able to:* describe the concepts of the Mastery Rubric* identify the KSAs and Stages* describe the concepts of the Performance Level Descriptors (PLDs)* start to use the MR-Bi could be applied to your courses and/or Professional developmental trajectory

Abstract: The recorded presentation introduces the Mastery Rubric for Bioinformatics, describing its structure and how it charts performance as learners traverse a...

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...

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 2: miFISH chr2 Replicate 2)

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 2

Experiment Imaging Method: epifluorescence microscopy
Protocol Name: iFISH protocol

Each dataset consists of multiple...

Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH (Dataset 2: miFISH chr2 Replicate 2)

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 2

Experiment Imaging Method: epifluorescence microscopy
Protocol Name: iFISH protocol

Each dataset consists of multiple...

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 3: miFISH with one dual-color probe AF594-AF488 and two single-color probes AT542 and AT647N)

Ana Faustino Mota, Maud Schweitzer & Magda Bienko
We performed a single colour experiment where one probe with alternated colours (AF488-AF594) 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...

Detailed feature profile of MirGeneDB highly and lowly expressed miRNA precursors

Wenjing Kang, Bastian Fromm, Inna Biryukova & Marc Friedländer
This is the Supplementary Data 9 of the MapToCleave study. ​​The file folder contains detailed feature information of MirGeneDB highly and lowly expressed miRNA precursors of 20 species. There are six feature files for each miRNA precursor. The file with the suffix “.statistics” provides basic information on the hairpin. The file with the suffix “.fold” provides RNA secondary structure in dot bracket format predicted by RNAfold. The file with suffix “.unopened_5p_ref” and “.unopened_3p_ref” provides positional...

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