230 Works

Single cell RNA sequencing data from: Clonal competition within complex evolutionary hierarchies shapes AML over time.

Carl Sandén, Henrik Lilljebjörn, Christina Orsmark Pietras, Rasmus Henningsson, Karim H. Saba, Niklas Landberg, Hanna Thorsson, Sofia Von Palffy, Pablo Peña-Martinez, Carl Högberg, Marianne Rissler, David Gisselsson, Vladimir Lazarevic, Gunnar Juliusson, Helena Ågerstam & Thoas Fioretos
10x genomics single cell RNA sequencing data (fastq-files) from three samples representing one AML and two xenografted samples.

Data from: AML Display Increased CTCF Occupancy Associated to Aberrant Gene Expression and Transcription Factor Binding

Huthayfa Mujahed, Andreas Lennartsson & Soren Lehmann
RNA-seq, ChIP-seq and Methylation array data from fifteen Acute Myeloid Leukemia patients and five normal donors.

Fluent Python nuggets. A brief presentation.

Per Kraulis
Some nuggets of Python coding wisdom out of the book Fluent Python by Lucian Ramalho. A light-weight presentation.

Life Science Data Management lecture

Niclas Jareborg
Video recording of a general lecture about Data Management practices for Life Science in three parts, and a pdf with the slides.
Note! The sound for the movie in part 3 doesn't work. Please go to the Youtube clip and watch it: https://www.youtube.com/watch?v=N2zK3sAtr-4.

Life Science Data Management lecture

Niclas Jareborg
Video recording of a general lecture about Data Management practices for Life Science in three parts, and a pdf with the slides.
Note! The sound for the movie in part 3 doesn't work. Please go to the Youtube clip and watch it: https://www.youtube.com/watch?v=N2zK3sAtr-4.

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!

StratFreshDB v1.1

Moritz Buck
Stratified lakes and ponds that feature steep oxygen gradients are known to be significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the resident microbial communities, especially in the oxygen-depleted hypolimnetic compartments are poorly known. In this paper, we present a comprehensive metagenome dataset including shotgun metagenomes from 29 stratified lakes and 12 ponds mainly located in the boreal and subarctic regions but also including one reservoir...

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...

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 6: iFISH chr2 spotting Replicate 1)

Ana Faustino Mota, Maud Schweitzer & Magda Bienko
We designed 21 probes targeting 21 consecutive loci on chromosome 2 using iFISH4U. The 23 loci are spaced with 10 Mb. There are 3 probes with AF488 dye, 3 probes with AT542, 3 probes with AF594, 3 probes with AT647N, 6 probes with AF700 and 3 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...

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...

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 7: iFISH chr2 spotting Replicate 2)

Ana Faustino Mota, Maud Schweitzer & Magda Bienko
We designed 21 probes targeting 21 consecutive loci on chromosome 2 using iFISH4U. The 23 loci are spaced with 10 Mb. There are 3 probes with AF488 dye, 3 probes with AT542, 3 probes with AF594, 3 probes with AT647N, 6 probes with AF700 and 3 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 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...

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...

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....

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...

HASTE miniTEM Example Images

Ben Blamey & Ida-Maria Sintorn
Series of images of a sample of kidney tissue captured from the miniTEM (a 25keV transmission electron microscope) at Vironova offices in Stockholm (2019-02-04), for purposes of testing software related to the HASTE project (http://haste.research.it.uu.se/).
The dataset consists of 759 8-bit greyscale PNG images.

Used in this publication (and others):
Resource- and Message Size-Aware Scheduling of Stream Processing at the Edge with application to Realtime MicroscopyBen Blamey, Ida-Maria Sintorn, Andreas Hellander, Salman Toorhttps://arxiv.org/abs/1912.09088
Also"Rapid development of cloud-native intelligent data...

HASTE miniTEM Example Images

Ben Blamey & Ida-Maria Sintorn
Series of images of a sample of kidney tissue captured from the miniTEM (a 25keV transmission electron microscope) at Vironova offices in Stockholm (2019-02-04), for purposes of testing software related to the HASTE project (http://haste.research.it.uu.se/).
The dataset consists of 759 8-bit greyscale PNG images.

Used in this publication (and others):
Resource- and Message Size-Aware Scheduling of Stream Processing at the Edge with application to Realtime MicroscopyBen Blamey, Ida-Maria Sintorn, Andreas Hellander, Salman Toorhttps://arxiv.org/abs/1912.09088
Also"Rapid development of cloud-native intelligent data...

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 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...

Detailed feature profile of MapToCleave processed and unprocessed miRNA precursors

Wenjing Kang, Bastian Fromm, Inna Biryukova & Marc Friedländer
This is the Supplemental Data 6 of the MapToCleave study.
The file folder contains detailed feature information of MapToCleave processed and unprocessed miRNA precursors. There are seven feature files for each miRNA precursor. The file with the suffix “.HEK.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 the suffix “.str” provides printed RNA secondary structure in txt...

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