37 Works

Modelling of Large Protein Complexes

Patrick Bryant & Arne Elofsson
AlphaFold and AlphaFold-multimer can predict the structure of single- and multiple chain proteins with very high accuracy. However, predicting protein complexes with more than a handful of chains is still unfeasible, as the accuracy rapidly decreases with the number of chains and the protein size is limited by the memory on a GPU. Nevertheless, it might be possible to predict the structure of large complexes starting from predictions of subcomponents. Here, we take a graph...

Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma

Lucia Pena-Perez & Robert Månsson
This repository contains 10x Chromium linked-read WGS (lrWGS), RNAseq and H3K27Ac ChIPseq from multiple myeloma.
The data consists of fastq files from lrWGS of 37 individuals with data from tumor and matched normal tissue from 32 of them. Additionally, it contains fastq files from RNAseq of 32 of the 37 patients and H3K27Ac ChIPseq data from select patients.
The data set contains sensitive human genomic data and is under restricted access. Request for...

Data and scripts for Mol Ecol article by Jahnke et al: Seascape genomics identify adaptive barriers correlated to tidal amplitude in the shore crab Carcinus maenas

Marlene Jahnke, Per-Olav Moksnes, Alan Le Moan, Gerrit Martens & Per R Jonsson
This repository includes data files and scripts used in the publication "Seascape genomics identify adaptive barriers correlated to tidal amplitude in the shore crab Carcinus maenas" published in Molecular Ecology in 2022.In this publication we assessed 12 sites in the native range of the European shore crab Carcinus maenas spanning >2000 km, and examined genetic structure and selection to tidal gradient using 24,000 Single Nucleotide Polymorphisms (SNPs) derived from 2b-RAD sequencing. Additionally, we performed biophysical...

Hyperthermia-induced in situ drug amorphization by superparamagnetic nanoparticles in oral dosage forms

Shaquib Rahman Ansari, Alexandra Teleki, Shno Asad, Nele-Johanna Hempel, Peter Svedlindh, Korbinian Lobmann & Christel AS Bergström
Superparamagnetic iron oxide nanoparticles (SPIONs) generate heat upon exposure to an alternating magnetic field (AMF) which has been studied for hyperthermia treatment and triggered drug release. This study introduces a novel application of magnetic hyperthermia to induce amorphization of a poorly aqueous soluble drug, celecoxib, in situ in tablets for oral administration. In situ amorphization can overcome the drug development hurdle of poor aqueous solubility by molecularly dispersing the drug in a polymeric network inside...

Morphological profiling of environmental chemical combinations - images, pipelines, and features

Jonne Rietdijk, Tanya Aggarwal, Polina Georgiev, Maris Lapins, Jordi Carreras-Puigvert & Ola Spjuth
Abstract: Environmental chemicals are commonly studied one at a time, and there is a need to advance our understanding of the effect of exposure to their combinations. Here we apply high-content microscopy imaging of cells stained with multiplexed dyes (Cell Painting) to profile the effects of Cetyltrimethylammonium bromide (CTAB), Bisphenol A (BPA), and Dibutyltin dilaurate (DBTDL) exposure on four human cell lines; both individually and in all combinations. We show that morphological features can...

Data and code related to \"Direct measurements of mRNA translation kinetics in living cells\", by Metelev et al.

Mikhail Metelev, Erik Lundin, Ivan L. Volkov, Arvid Heden Gynnå, Johan Elf & Magnus Johansson
This repository contains microscopy data and analysis code related to the publication: Metelev et al., "Direct measurements of mRNA translation kinetics in living cells".
The study includes single-particle tracking of ribosomal subunits in live E. coli cells, for analysis of translation kinetics under different conditions.
A detailed list of files and file organization can be found in the readme text file.

Single base substitution mutational signatures in pediatric acute myeloid leukemia based on whole genome sequencing

Rebeqa Gunnarsson, Minjun Yang, Linda Olsson Arvidsson, andrea Biloglav, Mikael Behrendtz, Anders Castor, Kajsa Paulsson & Bertil Johansson
This dataset includes whole genome sequencing (WGS) data of 20 diagnostic, and 20 remission samples from 20 children/adolescents with acute myeloid leukemia (AML), treated at the Departments of Pediatrics at Lund and Linköping University Hospitals between 1994 and 2016. The median age of the patients was 8 years (range 0-17 years) and the female/male ratio was 1:1. DNA was extracted from diagnostic bone marrow (BM; n = 17)/peripheral blood (PB; n = 3) samples, remission...

Targeted sequencing of 252 genes based on their relevance in lymphoid malignancies

Silvia Bonfiglio, Lesley-Ann Sutton, Viktor Ljungström, Antonella Capasso, Tatjana Pandzic, Simone Weström, Hassan Foroughi Asl, Aron Skaftason, Anna Gellerbring, Anna Lyander, Francesca Gandini, Gianluca Gaidano, Livio Trentin, Lisa Bonello, Gianluigi Reda, Csaba Bodor, Niki Stravoyianni, Costantine S. Tam, Roberto Marasca, Francesco Forconi, Panayiotis Panayiotidis, Ingo Ringshausen, Ozren Jakšić, Alessandra Tedeschi, Anna Maria Frustaci … & Paolo Ghia
Dataset description Data consists of CRAM file from capture-based gene panel sequencing (Twist Bioscience) of 252 genes selected based on their relevance in lymphoid malignancies. The panel also included genome-wide backbone probes for copy-number analysis. The preprared libraries were then subsequenlty equenced in paired-end mode (2x150bp) on the Illumina NovaSeq 6000 (Illumina Inc.). BALSAMIC was used to analyze the FASTQ files and aligning them to reference genome. Trimmed reads were mapped to the reference genome...

Hyperthermia-induced in situ drug amorphization by superparamagnetic nanoparticles in oral dosage forms

Shaquib Rahman Ansari, Alexandra Teleki, Shno Asad, Nele-Johanna Hempel, Peter Svedlindh, Korbinian Lobmann & Christel AS Bergström
Superparamagnetic iron oxide nanoparticles (SPIONs) generate heat upon exposure to an alternating magnetic field (AMF) which has been studied for hyperthermia treatment and triggered drug release. This study introduces a novel application of magnetic hyperthermia to induce amorphization of a poorly aqueous soluble drug, celecoxib, in situ in tablets for oral administration. In situ amorphization can overcome the drug development hurdle of poor aqueous solubility by molecularly dispersing the drug in a polymeric network inside...

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...

Data and scripts for Mol Ecol article by Jahnke et al: Seascape genomics identify adaptive barriers correlated to tidal amplitude in the shore crab Carcinus maenas

Marlene Jahnke, Per-Olav Moksnes, Alan Le Moan, Gerrit Martens & Per R Jonsson
This repository includes data files and scripts used in the publication "Seascape genomics identify adaptive barriers correlated to tidal amplitude in the shore crab Carcinus maenas" published in Molecular Ecology in 2022.In this publication we assessed 12 sites in the native range of the European shore crab Carcinus maenas spanning >2000 km, and examined genetic structure and selection to tidal gradient using 24,000 Single Nucleotide Polymorphisms (SNPs) derived from 2b-RAD sequencing. Additionally, we performed biophysical...

Single cell whole genome sequencing of high hyperdiploid acute lymphoblastic leukemia

Eleanor Woodward, Minjun Yang, Larissa Helena Moura-Castro, Hilda van den Bos, Rebeqa Gunnarsson, Linda Olsson Arvidsson, Diana C. J. Spierings, Anders Castor, Nicolas Duployez, Marketa Zaliova, Jan Zuna, Bertil Johansson, Floris Foijer & Kajsa Paulsson
This dataset was collected from viable bone marrow cells obtained at diagnosis from nine patients with high hyperdiploid ALL and one normal bone marrow sample. All samples were subjected to low pass single cell whole genome sequencing with the median sequencing coverage of 0.02x. Single nuclei in G0/G1 phase were isolated using a fluorescence-activated cell sorting (FACS) cytometer. DNA libraries were constructed and associated next-generation sequencing was carried out by European Research Institute for the...

Data and code related to \"Direct measurements of mRNA translation kinetics in living cells\", by Metelev et al.

Mikhail Metelev, Erik Lundin, Ivan L. Volkov, Arvid Heden Gynnå, Johan Elf & Magnus Johansson
This repository contains microscopy data and analysis code related to the publication: Metelev et al., "Direct measurements of mRNA translation kinetics in living cells".
The study includes single-particle tracking of ribosomal subunits in live E. coli cells, for analysis of translation kinetics under different conditions.
A detailed list of files and file organization can be found in the readme text file.

Targeted sequencing of 252 genes based on their relevance in lymphoid malignancies

Silvia Bonfiglio, Lesley-Ann Sutton, Viktor Ljungström, Antonella Capasso, Tatjana Pandzic, Simone Weström, Hassan Foroughi Asl, Aron Skaftason, Anna Gellerbring, Anna Lyander, Francesca Gandini, Gianluca Gaidano, Livio Trentin, Lisa Bonello, Gianluigi Reda, Csaba Bodor, Niki Stravoyianni, Costantine S. Tam, Roberto Marasca, Francesco Forconi, Panayiotis Panayiotidis, Ingo Ringshausen, Ozren Jakšić, Alessandra Tedeschi, Anna Maria Frustaci … & Paolo Ghia
Dataset description Data consists of CRAM file from capture-based gene panel sequencing (Twist Bioscience) of 252 genes selected based on their relevance in lymphoid malignancies. The panel also included genome-wide backbone probes for copy-number analysis. The preprared libraries were then subsequenlty equenced in paired-end mode (2x150bp) on the Illumina NovaSeq 6000 (Illumina Inc.). BALSAMIC was used to analyze the FASTQ files and aligning them to reference genome. Trimmed reads were mapped to the reference genome...

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...

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...

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...

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 whole genome sequencing of high hyperdiploid acute lymphoblastic leukemia

Eleanor Woodward, Minjun Yang, Larissa Helena Moura-Castro, Hilda van den Bos, Rebeqa Gunnarsson, Linda Olsson Arvidsson, Diana C. J. Spierings, Anders Castor, Nicolas Duployez, Marketa Zaliova, Jan Zuna, Bertil Johansson, Floris Foijer & Kajsa Paulsson
This dataset was collected from viable bone marrow cells obtained at diagnosis from nine patients with high hyperdiploid ALL and one normal bone marrow sample. All samples were subjected to low pass single cell whole genome sequencing with the median sequencing coverage of 0.02x. Single nuclei in G0/G1 phase were isolated using a fluorescence-activated cell sorting (FACS) cytometer. DNA libraries were constructed and associated next-generation sequencing was carried out by European Research Institute for the...

Modelling of Large Protein Complexes

Patrick Bryant & Arne Elofsson
AlphaFold and AlphaFold-multimer can predict the structure of single- and multiple chain proteins with very high accuracy. However, predicting protein complexes with more than a handful of chains is still unfeasible, as the accuracy rapidly decreases with the number of chains and the protein size is limited by the memory on a GPU. Nevertheless, it might be possible to predict the structure of large complexes starting from predictions of subcomponents. Here, we take a graph...

Single base substitution mutational signatures in pediatric acute myeloid leukemia based on whole genome sequencing

Rebeqa Gunnarsson, Minjun Yang, Linda Olsson Arvidsson, andrea Biloglav, Mikael Behrendtz, Anders Castor, Kajsa Paulsson & Bertil Johansson
This dataset includes whole genome sequencing (WGS) data of 20 diagnostic, and 20 remission samples from 20 children/adolescents with acute myeloid leukemia (AML), treated at the Departments of Pediatrics at Lund and Linköping University Hospitals between 1994 and 2016. The median age of the patients was 8 years (range 0-17 years) and the female/male ratio was 1:1. DNA was extracted from diagnostic bone marrow (BM; n = 17)/peripheral blood (PB; n = 3) samples, remission...

Data and code related to \"Direct measurements of mRNA translation kinetics in living cells\", by Metelev et al.

Mikhail Metelev, Erik Lundin, Ivan L. Volkov, Arvid Heden Gynnå, Johan Elf & Magnus Johansson
This repository contains microscopy data and analysis code related to the publication: Metelev et al., "Direct measurements of mRNA translation kinetics in living cells".
The study includes single-particle tracking of ribosomal subunits in live E. coli cells, for analysis of translation kinetics under different conditions.
A detailed list of files and file organization can be found in readme.pdf.

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...

Morphological profiling of environmental chemical combinations - images, pipelines, and features

Jonne Rietdijk, Tanya Aggarwal, Polina Georgiev, Maris Lapins, Jordi Carreras-Puigvert & Ola Spjuth
Abstract: Environmental chemicals are commonly studied one at a time, and there is a need to advance our understanding of the effect of exposure to their combinations. Here we apply high-content microscopy imaging of cells stained with multiplexed dyes (Cell Painting) to profile the effects of Cetyltrimethylammonium bromide (CTAB), Bisphenol A (BPA), and Dibutyltin dilaurate (DBTDL) exposure on four human cell lines; both individually and in all combinations. We show that morphological features can...

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...

Registration Year

  • 2022
    37

Resource Types

  • Dataset
    37