Find research datasets worth reusing

Particle-in-cell data in support of interchange reconnection paper

IDL programs (the .pro files) and data (the .dat file) to generate the simulation plots in "Interchange reconnection within coronal holes powers the solar wind".

FMPP and Testicular Germ Cell Tumors - Supplementary Data

Objective: The purpose of this study is to report development of a malignant testicular germ cell tumor (GCT) in two young adult males with Familial Male-limited Precocious Puberty (FMPP) due to (LHCGR) pathogenic variants in two families. Secondary, to study the possible relation between FMPP and testicular tumors and to investigate whether FMPP might predispose to development of malignant testicular tumors in adulthood a literature review is conducted. Methods: Data on six cases in two families are obtained from the available medical records. In addition, a database search is performed in Cochrane, Pubmed and Embase for studies that report on a possible link between FMPP and testicular tumors. Results: The characteristics of six males with FMPP based on activating luteinizing hormone receptor (LHCGR) germline pathogenic variants are described, as well as details of the testicular GCTs. Furthermore, literature review identified four more patients with signs of FMPP and a (precursor of a) testicular GCT in adolescence or adulthood (age 15 to 35 years). Additionally, twelve patients with signs of precocious puberty and, simultaneously, occurrence of a Leydig cell adenoma or Leydig cell hyperplasia are reported. Conclusion: There is a strong suggestion that FMPP might increase the risk of development of testicular GCTs in early adulthood compared to the risk in the general population. Therefore, prolonged patient monitoring from mid-pubertal age onwards including instruction for selfexamination and periodic testicular ultrasound investigation in patients with a germline LHCGRpathogenic variants might contribute to early detection and thus early treatment of testicular GCT. This files contains the supplementary data.

Raw output data from ColabFold modelling for the paper 'Interaction of C21ORF2 with a domain of NEK1 mutated in human diseases is vital for NEK1 function in human cells'

Raw output data from ColabFold modelling for the paper 'Interaction of C21ORF2 with a domain of NEK1 mutated in human diseases is vital for NEK1 function in human cells' File descriptions: NEK11160endC21ORF2_amber_2e60f_relaxed_rank_1_model_1_fixed.pdb ColabFold output PDB file - Rank 1 model NEK11160endC21ORF2_amber_2e60f_relaxed_rank_2_model_2_fixed.pdb ColabFold output PDB file - Rank 2 model NEK11160endC21ORF2_amber_2e60f_relaxed_rank_3_model_4_fixed.pdb ColabFold output PDB file - Rank 3 model NEK11160endC21ORF2_amber_2e60f_relaxed_rank_4_model_3_fixed.pdb ColabFold output PDB file - Rank 4 model NEK11160endC21ORF2_amber_2e60f_relaxed_rank_5_model_5_fixed.pdb ColabFold output PDB file - Rank 5 model NEK11160endC21ORF2_amber_2e60f_coverage.png ColabFold output chart - MSA sequence coverage NEK11160endC21ORF2_amber_2e60f_PAE.png ColabFold output chart - PAE for each model NEK11160endC21ORF2_amber_2e60f_plddt.png ColabFold output chart - predicted IDDT per position Supplementary Excel file 1 List of residues predicted to be involved in intermolecular interactions, and the type of interaction (based on PDB files for each models, generated using BIOVIA Discovery Studio 2021)

opencc-zeroSep 2022View details →

dryad36/100

Integrated plasma proteomic and single-cell immune signaling network signatures demarcate mild, moderate, and severe COVID-19

The biological determinants underlying the range of COVID-19 clinical manifestations are not fully understood. Here, over 1400 plasma proteins and 2600 single-cell immune features comprising cell phenotype, endogenous signaling activity, and signaling responses to inflammatory ligands are cross-sectionally assessed in peripheral blood from 97 patients with mild, moderate, and severe COVID-19 and 40 uninfected patients. Using an integrated computational approach to analyze the combined plasma and single-cell proteomic data, we identify and independently validate a multivariate model classifying COVID-19 severity (multi-class AUCtraining = 0.799, p-value = 4.2e-6; multi-class AUCvalidation = 0.773, p-value = 7.7e-6). Examination of informative model features reveals novel biological signatures of COVID-19 severity, including the dysregulation of JAK/STAT, MAPK/mTOR, and NF-κB immune signaling networks in addition to recapitulating known hallmarks of COVID-19. These results provide a set of early determinants of COVID-19 severity that may point to therapeutic targets for prevention and/or treatment of COVID-19 progression.

opencc-by-4.0Apr 2022View details →

Bulk NGS/allele quantification - Highly efficient generation of isogenic pluripotent stem cell models using prime editing

This file contains sequencing results for bulk NGS and amplicons covering specific regions of interest related to prime editing of hPSCs.

opencc-by-4.0Jul 2022View details →

Highly efficient generation of isogenic pluripotent stem cell models using prime editing - Datasets

This collection contains the following datasets: 1. AAVS1 knock-in genotyping 2. aCGH karyotyping 3. Tabular datasets for associated graphical figures

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Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity models (NMR datasets, maternal plasma and infant brain)

Maternal obesity during pregnancy is associated with neurodevelopmental disorder (NDD) risk. We utilized integrative multi-omics to examine maternal obesity effects on offspring neurodevelopment in rhesus macaques by comparison to lean controls and two interventions. Differentially methylated regions (DMRs) from longitudinal maternal blood-derived cell-free fetal DNA (cffDNA) significantly overlapped with DMRs from infant brain. The DMRs were enriched for neurodevelopmental functions, methylation-sensitive developmental transcription factor motifs, and human NDD DMRs identified from brain and placenta. Brain and cffDNA methylation levels from a large region overlapping mir-663 correlated with maternal obesity, metabolic and immune markers, and infant behavior. A DUX4 hippocampal co-methylation network correlated with maternal obesity, infant behavior, infant hippocampal lipidomic and metabolomic profiles, and maternal blood measurements of DUX4 cffDNA methylation, cytokines, and metabolites. Ultimately, maternal obesity altered infant brain and behavior, and these differences were detectable in pregnancy through integrative analyses of cffDNA methylation with immune and metabolic factors.

opencc-zeroAug 2022View details →

Common anti-cancer therapies induce somatic mutations in stem cells of healthy tissue

Genome-wide mutation analyses have revealed that specific anti-cancer drugs are highly mutagenic to cancer cells, but the mutational impact of anti-cancer therapies on normal cells is not known. Here, we examine genome-wide somatic mutation patterns in 42 healthy adult stem cells (ASCs) of the colon or the liver from 14 colorectal cancer patients (mean of 3.2 ASC per donor) that received systemic chemotherapy and/or radiotherapy. The platinum-based chemo-drug Oxaliplatin induces on average 535±260 mutations in colon ASC, while 5-FU shows a complete mutagenic absence in most colon ASCs. In contrast with the colon, normal liver ASCs escape mutagenesis from systemic treatment. Radiation results in the accumulation of 50-100 5-10,000bp deletions and structural rearrangements in colon ASCs. Thus, while chemotherapies are highly effective at killing cancer cells, their systemic use also increases the mutational burden of long-lived normal stem cells responsible for tissue renewal thereby increasing the risk for developing second cancers.

opencc-by-4.0Feb 2023View details →

T-cell receptor Vβ (TCRVB) deep sequencing on human T cells isolated from humanized mice engrafted with human PBMC and treated or not with PTCy post-transplantation

Nucleotide sequence data of  TCRVB sequencing performed on T cells isolated from the pre-transplantation hPBMC (donor T cells) or from mice organs at day 21 post-transplantation (injected or not with PTCy at day 3) to determine the impact of PTCy on the T cell V beta (TCRVB) receptor repertoire diversity. NSG mice were engrafted with human PBMC to develop xeno-GVHD and treated or not with 100 mg/kg PTCy. Spleens and lungs from 10 NSG mice per group were pooled and stained to sorted  human CD4+ and CD8+ . DNA of human CD4+ and CD8+ T cells sorted from each organ and  from the PBMC donor was extracted. One hundred fifty µg from each sample were used for T-cell receptor Vβ (TCRVB) deep sequencing performed by Adaptive Biotechnologies.

Heterogeneity of RNA editing in mesothelioma and how RNA editing enzyme ADAR2 affects mesothelioma cell growth, response to chemotherapy and tumor microenvironment

Raw data supporting the manuscript

Long-term testing of alkaline electrolyser single cell using Raney Ni electrodes

Chronopotentiometry and polarization curves of alkaline electrolyser single cell using Raney Ni electrodes.

opencc-zeroSep 2022View details →

dryad36/100

Dictyostelium discoideum cells retain nutrients when the cells are about to outgrow their food source

Dictyostelium discoideum is a unicellular eukaryote that eats bacteria, and eventually overgrows the bacteria. D. discoideum cells accumulate extracellular polyphosphate (polyP), and the polyP concentration increases as the local cell density increases. At high cell densities, the correspondingly high extracellular polyP concentrations allow cells to sense that they are about to overgrow their food supply and starve, causing the D. discoideum cells to inhibit their proliferation. In this report, we show that high extracellular polyP inhibits exocytosis of undigested or partially digested nutrients. PolyP decreases plasma membrane recycling and apparent cell membrane fluidity, and this requires the G protein-coupled polyP receptor GrlD, the polyphosphate kinase Ppk1, and the inositol hexakisphosphate kinase I6kA. PolyP alters protein contents in detergent-insoluble crude cytoskeletons, but does not significantly affect random cell motility, cell speed, or F-actin levels. Together, these data suggest that D. discoideum cells use polyP as a signal to sense their local cell density and reduce cell membrane fluidity and membrane recycling, perhaps as a mechanism to retain ingested food when the cells are about to starve.

Supplementary data for article "Reduced B-cell antigenicity of Omicron lowers host serologic response"

This repository contains five supplementary data files for the research article "Reduced B-cell antigenicity of Omicron lowers host serologic response". For more information, please refer to the article preprint https://doi.org/10.1101/2022.02.15.480546 and upcoming article at Cell Reports.   <ol> <li>Table_hCoV229E.xlsx: list of hCoV229E RBD sequences, with associated isolate and collection date identifiers, and ScanNet antigenicity score for reproducing Figure 3A. Aligned sequences and templates are also provided.</li> <li>table_artificial_variants.csv: List of artificial RBD sequences generated by an evolutionary-based sequence generative model for reproducing Figure 3B, Supplementary Figure S6H.</li> <li>MSA_RBD.fasta: Multiple Sequence Alignment of RBD sequences and sample weights used for training the sequence generative model used in Figure 3B, Supplementary Figures S2C, S6.</li> <li>table_antibody_hit_rate_RBD.csv: Empirical epitope distribution for the RBD, as determined from the Protein Data Bank and raw data for Supplementary Figure S1).</li> <li>RBD_virtual_DMS.xlsx: virtual Deep Mutational Scan performed with ScanNet and the sequence generative model shown in Supplementary Figure S2.</li> </ol>

Gene expression counts from amniotic fluid cells

File description: <ol> <li> Gene-level counts using the gtf file from the release 29 of GENCODE <a href="https://www.gencodegenes.org/human/release_29">https://www.gencodegenes.org/human/release_29</a> </li> <li> Split counts spanning from one exon to another using an annotation-free algorithm, therefore capturing new splice sites </li> <li> Non-split counts covering exon-intron boundaries </li> <li> Sample annotation describing each sample from the dataset </li> <li> Description file with global information from the dataset </li> </ol> Use: The count matrices are intended to help researchers that are interested in using RNA-Seq data with the purpose of diagnostics. Researchers can merge their own dataset with the downloaded ones, provided the tissue, genome build, strand, and paired end specifications match. Afterwards, the DROP pipeline can be used to compute expression and splicing outliers (<a href="https://github.com/gagneurlab/drop">https://github.com/gagneurlab/drop</a>). Maintainer: Vicente A. Yépez, <a href="mailto:yepez@in.tum.de">yepez@in.tum.de</a> Title: Gene expression and splicing counts from amniotic fluid cells Number of samples: 56 Tissue: Amniotic fluid cells Organism: Homo sapiens Genome assembly: hg19 Gene annotation: gencode29 Disease ICD-10: Q89: F2100984A and F2100985, Q23: F1901567 and Q74: F2000845 Strand specific: False Paired end: True Cite as: Cite both the resource using Zenodo's citation and the publication under References Dataset contact: Brian Chung bhychung@hku.hk Comments: A total of 56 RNA-seq samples were used for running pipeline. Out of those, 52 samples were included in the manuscript.

opencc-by-4.0Mar 2022View details →

Single cell whole genome sequencing from Funnell, O'Flanagan, Williams et al

This repository provides the processed data necessary to reproduce the results from: "Single cell genomic variation induced by mutational processes in cancer Funnell, O’Flanagan, Williams et al" This includes the following: <ul> <li>Single cell whole genome sequencing <ul> <li>Allele specific copy number profiles</li> <li>SNV counts per cell</li> <li>Structural variant counts per cell</li> <li>QC metrics</li> <li>clone assignments</li> <li>phylogenetic trees computed with sitka</li> <li>benchmarking results vs other methods</li> </ul> </li> <li>bulk whole genome sequencing <ul> <li>copy number profiles</li> <li>SNVs</li> </ul> </li> <li>10X single cell RNA sequencing <ul> <li>count matrices</li> <li>seurat Rdata objects</li> </ul> </li> <li>analysis tables <ul> <li>downstream processed results used to generate figures</li> </ul> </li> <li>oxford nanopore <ul> <li>phasing results</li> </ul> </li> </ul>   For further information please feel free to get in touch with Marc Williams (william1 [at] mskcc.org)

Single-cell transcriptome analysis of the in vivo response to viral infection in the cave nectar bat Eonycteris spelaea

Bats are reservoir hosts of many zoonotic viruses with pandemic potential in humans. Here, we utilized single-cell transcriptome sequencing (scRNA-seq) to provide detailed comparative analyses of the immune repertoire and the transcriptional responses in the bat lungs upon in vivo infection with a double-stranded RNA virus, Pteropine orthoreovirus PRV3M. Neutrophils were observed to have basally high IDO1 expression, uniquely amongst mammals currently profiled by scRNA-seq. NK/T cells were the most abundant immune cell type in lung tissue, and included three distinct CD8 + effector T cell populations delineated by the differential expression of KLRB1, GFRA2 and DPP4. We identified NK/T clusters which up-regulated genes involved in T-cell activation and effector function early after viral infection. Alveolar macrophages and classical monocytes were key drivers of antiviral interferon signaling. Infection also resulted in the expansion of a CSF1R + population expressing collagen-like genes, which became the predominant myeloid cell type after infection. This work uncovers novel features relevant to viral disease tolerance in bats, lays a foundation for future in vivo and in vitro experimental investigations, and serves as a key resource for comparative immunology studies across bats and other mammals.   This upload is the transcriptome fasta file used for alignment for the dataset.

Exploring cell diversity and fidelity in crustacean limb regeneration using single-nucleus RNA sequencing

R objects containing datasets generated by snRNA-seq on Parhyale hawaiensis limbs. These datasets have been generated during my Phd thesis.

Autophagosomal/autolysosomal/lysosomal dynamics of FaDu and HGFb cells affected by autophagy modulators (dataset of dual labeling of autophagosomes and labeling lysosomes, confocal microscopy)

In this dataset, the impact of autophagy modulators on the auophagosomes and lysosomes in FaDu and HGF cells was investigated. Experimental details are described in the accompanying paper. This dataset contains total 702 CZI confocal image Z-stacks. Relevant paper: HANELOVA, Klara, RAUDENSKA, Martina, KRATOCHVILOVA, Monika, NAVRATIL, Jiri, VICAR, Tomas, BUGAJOVA, Maria, GUMULEC, Jaromir, MASARIK, Michal and BALVAN, Jan. Autophagy modulators influence the content of important signalling molecules in PS-positive extracellular vesicles. Cell Communication and Signaling. 24 May 2023. Vol. 21, no. 1, p. 120. DOI <a href="https://doi.org/10.1186/s12964-023-01126-z">10.1186/s12964-023-01126-z</a>. <div> <div> <div> </div> </div> </div> Model cell lines   The cell line FaDu (HTB-43TM), derived from a squamous cell carcinoma (SCC) of the hypopharynx, and the human gingival fibroblast cell line HGF (derived from the histologically normal gingival biopsy) were used in this study. The authenticated cell lines were purchased from the American Type Culture Collection (ATCC; Manassas, Virginia, USA) within the last five years.  Autophagy modulation For autophagy modulation, FaDu cells were treated for 24 h with 5nM bafilomycin A1 (Sigma-Aldrich, B1793), 50 µM of hydroxychloroquine sulphate (Sigma-Aldrich, H0915), 100 µM of Cpd18 (Calbiochem), 50 nM of autophinib (Sigma, SML2632), 10 µM of EACC (MedChemExpress), 200 nM of rapamycin (Sigma-Aldrich, R0395), 3 nM of Torin-1 (MedChemExpress), or 30 nM of NVP-BEZ235 (MedChemExpress). To induce starvation, cells were cultured in DMEM F12 without glutamine and without FBS (Biosera). Modulation of autophagy did not reduce the viability  of FaDu cells. Conditioned media preparation see details in the accompanying paper Fluorescence Microscopy The autophagosomal/autolysosomal/lysosomal dynamics of affected cells were observed using the combination of PremoTM Autophagy Tandem Sensor (P36239, Invitrogen) with the far-red emitting LysoTracker® Deep Red (L12492, Invitrogen) (Ex 647 nm/Em 668 nm). By combining acid-sensitive Emerald GFP (Ex 488 nm/Em 509 nm) with acid-insensitive TagRFP (Ex 555 nm/Em 584 nm) in the PremoTM kit, autophagosomes and autolysosomes labelling (yellow and red, respectively) is possible. Immediately after transduction with 12 µl PremoTM Autophagy Tandem Sensor/2ml cell suspension, cells were seeded at 5 × 105 into 35-mm glass-bottomed gelatin-coated dishes (Ibidi, μ-Dish 35 mm, high Glass Bottom) and cultured for 48 h to equilibrate expression levels. Subsequently, cells were exposed to the selected agents for 6, 12, 24 and 48 hours before imaging.  LysoTracker® Deep Red staining was performed 1 h before imaging.  To monitor the uptake of isolated PS-EVs by fibroblasts, we stained EVs with PKH67 (Sigma, PKH67GL) and then removed the remaining dye using Exosome Spin Columns (MW 3000) (Thermo Scientific, #4484449). The stained EVs were then suspended in 400 ul of cultivation medium and added to HGFB cells growing for 24 h in Ibidi µ-Slide I Luer (Ibidi, 80176). Image acquisition was performed 24 hours after EVs addition. 1 µl of 1 µg/ml of Hoechst 33342 (Enzo) (Ex 350 nm/ Em 461 nm) nuclear stain was added 1 hour before imaging. To determine the viability of the cell population prior to isolation of EVs, cells were left in a culture dish with 1 ml of culture medium to which propidium iodide (Sigma-Aldrich) and Hoechst 33342 were added 45 minutes before capturing.  To maximize the possibility of comparison between samples, all samples (from a single cell line) were captured on the same day in a single run using the same microscope settings. For each time and each treatment, 10–12 fields of view were captured from randomized sites of the culture dish. Epifluorescent microscopy images and confocal microscopy images were acquired using Laser scanning confocal microscope Zeiss LSM 880 with AiryscanFast module (Carl Zeiss Inc.) using a C-apochromat 40x/1.20 W and C-Apochromat 63 /1.20 W. LysoTracker® Deep Red was excited HeNe 633 nm solid-state laser and emitted light was detected at 638–759 nm. Emerald GFP was excited 488 nm ArgonRemote laser, and emitted light was detected at 493–576 nm. TagRFP was excited DPSS 561 nm laser, and emitted light was detected at 570–650 nm. Hoechst 33342 was excited with a 405 nm solid-state laser, and emitted light was detected at 410–508 nm. Fluorescence images were acquired by the transmitted light detector.  Images were analyzed using ImageJ software and custom MATLAB software developed in our laboratory. The analysis process consists of the segmentation of cells from the background and extraction of the intensity of fluorescence channels (TagRFP, GFP, LysoTracker) inside cells. For segmentation, a thresholding-based method was used, where a manually selected threshold was applied. Segmentation was applied to the image created as the sum of all fluorescence channels to achieve segmentation independent of the intensity of individual channels. To achieve better segmentation without noisy pixels, fluorescence images were preprocessed with median filter (7x7) and Gaussian filter (standard deviation 1); additionally, binary segmentation was post-processed with morphological closing and removal of small binary connected components (<5000px). For intensity extraction, the mean value of segmented cell pixels was used for each field of view. Besides individual fluorescence channels, the mean colocalization of TagRFP and GFP was calculated with a pixel-wise multiplication of TagRFP and GFP channels. File Naming CZI images are organised in folders according to cell line, treatment time, and treatment. Names include magnification, cell line measured, treatment, and time of treatment, <blockquote> 40x_FADU_BAF_12h_BF_4.czi </blockquote> The abbreviations used for treatments are as follows: BAF, bafilomycin A1; HCQ, hydroxychloroquine sulphate; Cpd18; APB, autophinib; EACC; RAPA, rapamycin; TOR1, Torin-1; BEZ, NVP-BEZ235; starv, starvation;

opencc-by-4.0Oct 2022View details →

A model for the dissemination of circulating tumour cell clusters involving platelet recruitment and a plastic switch between cooperative and individual behaviours

This folder includes live/dead cell counts as well as transwell assay data for the corresponding manuscript.