Find research datasets worth reusing

openmit-licenseNov 2023View details →

Paper data and code of manuscript: Intraspecific variation on heat tolerance in a model ectotherm: effects of body mass, cell size, oxygen and sex

When using the data or code from this manuscript, please cite it as:Leiva FP, Santos M, Rezende E, & Verberk WCEP. 2021. Paper data and code of manuscript: Intraspecific variation on heat tolerance in a model ectotherm: effects of body mass, cell size, oxygen and sex. Zenodo. <a href="https://doi.org/10.5281/zenodo.5120028">https://doi.org/10.5281/zenodo.5120028</a>.

opencc-by-4.0Oct 2023View details →

Host-guest complexation in wide bandgap perovskite solar cells

Wide bandgap hybrid halide perovskites are increasingly relevant in the fabrication of tandem solar cells. However, their efficiency and stability during operation are still limited by several factors, among which ion migration at the interface with charge-selective extraction layers is one of the most detrimental ones. Herein, we employ a host-guest complexation strategy to control interfacial ion migration by using dibenzo-21-crown-7 in wide bandgap hybrid halide perovskites based on methylammonium (MA) lead bromide. We demonstrate the capacity of the crown ether to affect the performances and stabilities of MAPbBr3 solar cells. As a result, we achieve power conversion efficiencies up to 5.9% with an open circuit voltage as high as 1.5 V, which is accompanied by stability over 300 h at 85 °C under nitrogen atmosphere, as well as more than 300 h at ambient temperature, maintaining ∼80% of initial performance. This represents a versatile strategy for wide bandgap photovoltaic devices.

Micro-CT image of cell-populated collagen scaffold in the aqueous environment (contrasted with PTA)

A dataset of the collagen scaffold populated with the 3T3 cells scanned in the aqueous environment using Bruker Skyscan 1276 machine (Bruker, Belgium). Scaffold productionThe processes of obtaining and working with collagen scaffolds were conducted in an isolated environment under sterile conditions. The collagen sponge matrix was manufactured at the Center for Collagen Innovation within the Institute of Regenerative Medicine at Sechenov University and provided to us for experimental purposes. In order to obtain the collagen, the authors utilized animal-derived materials sourced from the tendons of large horned cattle. To do this, the tendons were cleaned of excess tissues, cut into pieces with a thickness of 0.5-1 cm, and sequentially treated for 12 hours in a 0.5 M NaCl solution. Subsequently, the mass was homogenized in a 0.83 M acetic acid solution. The resulting suspension was hydrolyzed with 0.24% pepsin for 2 days, after which 1 M NaOH was added to adjust the pH to 7.5, halting the hydrolysis process. The suspension was precipitated with a 12% NaCl solution, the resulting precipitate was redissolved in 0.02 M acetic acid, and then dialyzed. To obtain collagen porous matrices (sponges), the obtained solution was neutralized using 0.1 M NaOH until a pH of 7-7.5 was reached, and the resulting suspension was lyophilized at -40°C for 2 days.Subsequently, the collagen matrix was cut into cubes with sides measuring 0.5 cm. These cubes were placed in 15 ml test tubes filled with 70% ethyl alcohol for sterilization. The test tubes were then placed on a shaker and left in the refrigerator at +4°C for 24 hours. Afterward, the collagen matrices were removed from the alcohol and rinsed five times with 0.9% NaCl.Following the alcohol rinse to confirm the absence of toxicity, an elution test, adapted following the ISO 10993 protocol, was conducted. To obtain collagen cube extracts, they were incubated in a cell culture medium at a volume of 1 ml per sample for 24 hours at 37°C. The 3T3 cell culture was passaged, with 5000 cells seeded in each well of a 96-well plate. After 24 hours, the cells were treated with extract at a volume of 200 µl per well and left in the incubator at 37°C for 24 hours. The following day, extracts were collected, and AlamarBlue reagent (Invitrogen, Waltham, MA, USA) was added according to the manufacturer's instructions to assess the metabolic activity of the cells. Serial dilutions of sodium dodecyl sulfate (SDS) were used as the positive control. Fluorescence intensity was measured using a Victor Nivo spectrofluorimeter (PerkinElmer, Waltham, Massachusetts, USA) at an excitation wavelength of 530 nm and an emission wavelength of 590 nm.Cell seedingAfter confirming the absence of cytotoxic effects, collagen sponges were seeded with the NIH 3T3 cell line at a density of 50,000 cells per sample (cubes of collagen sponge measuring 0.5 cm per side). Staining techniqueFixed specimens in 10% formalin with PBS were washed after 24 hours with distilled water and after that placed in 3% phosphotungstic acid dissolved in distilled water for 24 hours and kept on the rotary shaker at room temperature. After staining, samples were washed and stored in distilled water at 5 °C. Image acquisition and reconstructionA plastic tube filled with distilled water containing the contrasted sample was placed on the sample holder in a SkyScan 1276 micro-CT (Bruker, Kontich, Belgium) and were scanned at 3 μm voxel resolution with 70 kV voltage and 200 uA source power and an aluminum filter with 1 mm of thickness. The rotation was set to 360° around the vertical axis of the sample, with two middle frames for each 0.2° angle step.After scanning, the data were reconstructed using Bruker's NRecon software. During reconstruction, the ring artifact reduction value was set to 20% and the beam hardening correction value to 30%. After that, samples were exported as a series of 16-bit TIFF images which could be opened in the specialized software.

Sex and Age Impact CD4+ T Cell Susceptibility to HIV In Vitro Through Cell Activation Dynamics

Cellular composition and the responsiveness of the immune system evolve upon aging and are influenced by biological sex. CD4+ T cells from women living with HIV exhibit a decreased viral replication ex vivo compared to men's. We, thus, hypothesized that these findings could be recapitulated in vitro and infected primary CD4+ T cells with HIV-based vectors pseudotyped with VSV-G or HIV envelopes. We used cells isolated from twenty donors to interrogate the effect of sex and age on permissiveness over a six-day activation kinetics. Our data identified an increased permissiveness to HIV between 24 and 72 h post-stimulation. Sex- and age-based analyses at these time points showed an increased susceptibility to HIV of the cells isolated from males and from donors over 50 years of age, respectively. A parallel assessment of surface markers' expression revealed higher frequencies of activation marker CD69 and of immune checkpoint inhibitors (PD-1 and CTLA-4) in the cells from highly permissive donors. Furthermore, positive correlations were identified between the expression kinetics of CD69, PD-1 and CTLA-4 and HIV expression kinetics. The cell population heterogeneity was assessed using a single-cell RNA-Seq analysis and no cell subtype enrichment was identified according to sex. Finally, transcriptomic analyses further highlighted the role of activation in those differences with enriched activation and cell cycle gene sets in male and older female cells. Altogether, this study brought further evidence about the individual features affecting HIV replication at the cellular level and should be considered in latency reactivation studies for an HIV cure.

Reference model and embedding for human kidney endothelial cell mapping

Reference model and embedding for human kidney endothelial cell mappingThe reference model serves as a basis for the mapping of new data to the HLCA using scArches (Lotfollahi et al., https://doi.org/10.1038/s41587-021-01001-7).

Transcriptional profiling of peripheral blood mononuclear cells identifies inflammatory phenotypes in ataxia telangiectasia

This is an AnnData object in h5ad (hdf5) format containing de-identified bulk RNA-seq gene expression matrices from PBMCs. These data are related to the study entitled "Transcriptional profiling of peripheral blood mononuclear cells identifies inflammatory phenotypes in ataxia telangiectasia". This AnnData object contains a table of sample-specific metadata (`obs`), gene-specific metadata (`var`), and multiple gene expression matrices stored as `layers`. These layers include raw counts, DEseq2 normalized counts, vst normalized counts, and rlog normalized counts. Some additional layers include regressed versions of the previously mentioned counts matrices, where sequencing batch (`cohort` in the obs table) has been regressed out using the `combat` tool. The layer `rlog_combat_regressed_batch` is recommended for downstream processing, and has been loaded into the `X` slot of the anndata object for convenience. The md5sum of this h5ad file is listed here: 04d7c6c549fb37cf730a5dca7897f86fOpening and working with AnnData objects in h5ad format requires the use of the `anndata` python library (https://github.com/scverse/anndata).

Aquaporins Embedded in a Cell Membrane with O2 Diffusion

This is an illustration of an aquaporin  embedded in a cell membrane with O2 diffusion as well.

opencc-by-4.0Jun 2023View details →

Mural cells sustain a homeostatic vascular macrophage niche limiting chronic inflammation

If you use any of these data, please cite the corresponding publication:<a href="https://doi.org/10.1016/j.immuni.2023.08.002">Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation</a> <a href="https://doi.org/10.1016/j.immuni.2023.08.002">Pekayvaz et al., Immunity, 2023</a> . ( <a href="https://doi.org/10.1016/j.immuni.2023.08.002">https://doi.org/10.1016/j.immuni.2023.08.002</a> )scRNA-seq dataprocessed:processed_kidney_seurat.Rds processed_lung_seurat.Rdscount matrices:sample_M1_raw_feature_bc_matrix.h5 sample_M2_raw_feature_bc_matrix.h5script:process_sctransform.Rfunctions.R with helper functions (mainly for plotting) used in the process-script.RNA-seqmacrophages:macs_control_vs_knockout.hisat2.DirectDESeq2.tsv|xlsx (count data and DESeq2 results)aorta:aorta_control_vs_knockout.hisat2.DirectDESeq2.tsv|xlsx (count data and DESeq2 results)Dead vs. Living:peri_Dead_vs_Living.exon_all.DirectDESeq2.tsv|xlsx (count data and DESeq2 results)

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Anabaena circadian clock behavior under nitrogen-poor conditions from single-cell measurements of fluorescence intensity

Circadian clock arrays in multicellular filaments of the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120 display remarkable spatio-temporal coherence under nitrogen-replete conditions. To shed light on the interplay between circadian clocks and the formation of developmental patterns, we followed the expression of a clock-controlled gene under nitrogen deprivation, at the level of individual cells. Our experiments showed that differentiation into heterocysts took place preferentially within a limited interval of the circadian clock cycle, that gene expression in different vegetative intervals along a developed filament was discoordinated, and that the circadian clock was active in individual heterocysts. Furthermore, Anabaena mutants lacking the kaiABC genes encoding the circadian clock core components produced heterocysts but failed in diazotrophy. Therefore, genes related to some aspect of nitrogen fixation, rather than early or mid-heterocyst differentiation genes, are likely affected by the absence of the clock. A bioinformatics analysis supports the notion that RpaA may play a role as master regulator of clock outputs in Anabaena, the temporal control of differentiation by the circadian clock and the involvement of the clock in proper diazotrophic growth. Together, these results suggest that under nitrogen-deficient conditions, the clock coherent unit in Anabaena is reduced from a full filament under nitrogen-rich conditions to the vegetative cell interval between heterocysts.

opencc-zeroDec 2023View details →

opencc-by-4.0Dec 2022View details →

Dataset from the analysis of biological activity of endophytic strain Serratia quinivorans KP32, the expression of biocontrol-related genes and the activity of antioxidant enzymes in bacterial cells treated with pathogenic fungi filtrates

This dataset contains the data from the analyses published in the article entitled "Genetic Determinants of Antagonistic Interactions and the Response of New Endophytic Strain Serratia quinivorans KP32 to Fungal Phytopathogens" in the International Journal of Molecular Sciences (https://doi.org/10.3390/ijms232415561). The data consist of results collected for studies on the antifungal activity of KP32 strain towards four fungal phytopathogens, results of primer efficiency determination and studies on the expression of genes potentially involved in biocontrol after treatment of KP32 strain with the fungal phytopathogens filtrates. Additionally, absorbances from activity tests for catalase (CAT) and superoxide dismutase (SOD) in the strain treated with fungal pathogens are included.

Processed data to accompany "Clonally heritable gene expression imparts a layer of diversity within cell types"

This is the processed data underlying the paper "Clonally heritable gene expression imparts a layer of diversity within cell types" by Mold, Weissman, et al.  Data has been gone through preprocessing steps, using the Python Notebooks found at <a href="https://github.com/MartyWeissman/ClonalOmics/tree/main/Data">https://github.com/MartyWeissman/ClonalOmics/tree/main/Data</a>.   Smaller files are provided in .csv (comma-separated-value) format and larger files such as expression matrices are provided in .loom format (<a href="https://anndata.readthedocs.io/en/latest/">using the AnnData package</a>).

Single cell analysis by Quantitative image-based cytometry (QIBC)

Quantitative image-based cytometry (QIBC): Employing automated multichannel wild-field microscopy using the Olympus ScanR screening system. This system includes an inverted motorized Olympus IX83 microscope, a motorized stage, IR-laser hardware autofocus, a fast emission filter wheel with single band emission filters.  Images were analyzed and processed using ScanR analysis software and TIBCOSpotfire software was used to plot total nuclear pixel intensities and mean (total pixel intensities divided by nuclear area) nuclear intensities.

Molecular features of luminal breast cancer defined through spatial and single-cell transcriptomics (codes and data files)

This dataset includes all the relevant codes and data files associated with the paper ("Molecular features of luminal breast cancer defined through spatial and single-cell transcriptomics") in Clinical and Translational Medicine journal.

opencc-zeroJan 2024View details →

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Data from: Cellects, a software to quantify cell expansion and motion

Automated quantification offers unique opportunities to study biological phenomena, increasing reproducibility, replicability, accuracy, and throughput, while reducing observer biases. We present Cellects, a tool to quantify growth and motion in 2D. This software operates with image sequences containing specimens growing and moving on an immobile flat surface. Its user-friendly interface makes it easy to adjust the quantification parameters to cover a wide range of species and conditions, and includes tools to validate the results and correct mistakes if necessary. The software provides the region covered by the specimens at each point of time, as well as many geometrical descriptors that characterize it. We validated Cellects with Physarum polycephalum, which is particularly difficult to detect because of its complex shape and internal heterogeneity. This validation covered five different conditions with different background and lighting, and found Cellects to be highly accurate in all cases. Cellects' main strengths are its broad scope of action, automated computation of a variety of geometrical descriptors, easy installation and user-friendly interface.

opencc-by-4.0Oct 2023View details →

Machine learning links T cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer

Data supporting the findings of "<a href="https://doi.org/10.1158/2326-6066.CIR-23-0873" target="_blank" rel="noopener">Machine learning links T cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer</a>" publication. Files include patient and tissue region metadata (in metadata folder) and output of multiplex immunohistochemistry computational image processing workflow for each tissue region (in mIHC_files folder). The code used to produce the results of this study is available at: <a href="https://github.com/kblise/PDAC_mIHC_paper">https://github.com/kblise/PDAC_mIHC_paper</a>.

opencc-by-4.0Oct 2023View details →

Large-scale annotated dataset for cochlear hair cell detection and classification

Our sense of hearing is mediated by cochlear hair cells, of which there are two types organized in one row of inner hair cells and three rows of outer hair cells. Each cochlea contains 5 - 15 thousand terminally differentiated hair cells, and their survival is essential for hearing as they do not regenerate after insult. It is often desirable in hearing research to quantify the number of hair cells within cochlear samples, in both pathological conditions, and in response to treatment. Machine learning can be used to automate the quantification process but requires a vast and diverse dataset for effective training. In this study, we present a large collection of annotated cochlear hair-cell datasets, labeled with commonly used hair-cell markers and imaged using various fluorescence microscopy techniques. The collection includes samples from mouse, rat, guinea pig, pig, primate, and human cochlear tissue, from normal conditions and following in-vivo and in-vitroototoxic drug application. The dataset includes over 107,000 hair cells which have been manually identified and annotated as either inner or outer hair cells. This dataset is the result of a collaborative effort from multiple laboratories and has been carefully curated to represent a variety of imaging techniques. With suggested usage parameters and a well-described annotation procedure, this collection can facilitate the development of generalizable cochlear hair-cell detection models or serve as a starting point for fine-tuning models for other analysis tasks. By providing this dataset, we aim to give other hearing research groups the opportunity to develop their own tools with which to analyze cochlear imaging data more fully, accurately, and with greater ease. Associated code is provided here: https://github.com/indzhykulianlab/hcat-data

opencc-by-4.0Jan 2024View details →

From Pixels to Phenotypes: Integrating Image-Based Profiling with Cell Health Data Improves Interpretability

Code: https://github.com/srijitseal/BioMorph_Space Cell Painting assays generate morphological profiles that are versatile descriptors of biological systems and have been used to predict in vitro and in vivo drug effects. However, Cell Painting features are based on image statistics, and are, therefore, often not readily biologically interpretable. In this study, we introduce an approach that maps specific Cell Painting features into the BioMorph space using readouts from comprehensive Cell Health assays. We validated that the resulting BioMorph space effectively connected compounds not only with the morphological features associated with their bioactivity but with deeper insights into phenotypic characteristics and cellular processes associated with the given bioactivity. The BioMorph space revealed the mechanism of action for individual compounds, including dual-acting compounds such as emetine, an inhibitor of both protein synthesis and DNA replication. In summary, BioMorph space offers a more biologically relevant way to interpret cell morphological features from the Cell Painting assays and to generate hypotheses for experimental validation.   The following datasets are released:   Cell_Health_median_357_profiles_70_labels.csv : The Cell Heath dataset for CRISPR perturbations. Contains median consensus signatures for the 357 consensus profiles (119 CRISPR perturbations × 3 cell lines) Ref: Way et al. Cell_Painitng_CRISPR_Perturbations_357_profiles_827_features_scaled.csv: The Cell Painting dataset for CRISPR perturbations. Contains 827 morphology features (and metadata annotation) for 357 consensus profiles (119 CRISPR perturbations × 3 cell lines). Ref: Way et al. Cell_Painting_data_658_compounds_827_Features_scaled.csv The Cell Painting dataset for compound perturbations. Contains 658 structurally unique compounds with 827 Cell Painting features. Ref: Bray et al Endpoints_9_Mitotox_biological_activities_658_compounds.csv The biological assay activity labels for compound perturbations. Contains 658 structurally unique compounds with 9 biological activity consensus hit calls. Ref: ToxCast/MoleculeNet BioMoprh_pvalue_658_compunds_398_BioMorph_terms.csv: The dataset of standardised BioMorph term p-values. Contains 398 BioMorph terms for the 658 compounds in the biological activity dataset.  References:  Way et al. Predicting cell health phenotypes using image-based morphology profiling. Mol Biol Cell. 2021;32(9):995-1005. Bray et al. A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay. Gigascience. 2017;6(12):1-5.  MoleculeNet: Wu et al. MoleculeNet: A benchmark for molecular machine learning. Chem Sci. 2018;9(2):513-530.  ToxCast: Exploring ToxCast Data | US EPA https://www.epa.gov/chemical-research/exploring-toxcast-data (accessed Jul 9, 2023).

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Raw differential gene expression data, data S1, from: Molecular cascades and cell type-specific signatures in ASD revealed by single cell genomics

Genomic profiling in post-mortem brain from autistic individuals has consistently revealed convergent molecular changes. What drives these changes and how they relate to genetic susceptibility in this complex condition is not understood. We performed deep single nuclear RNA sequencing (snRNAseq) to examine cell composition and transcriptomics, identifying dysregulation of cell type-specific gene regulatory networks (GRNs) in autism, which we corroborated using snATAC-seq and spatial transcriptomics. Transcriptomic changes were primarily cell type-specific, involving multiple cell types, most prominently interhemispheric and callosal-projecting neurons, interneurons within superficial laminae, and distinct glial reactive states involving oligodendrocytes, microglia, and astrocytes. Autism-associated GRN drivers and their targets were enriched in rare and common genetic risk variants, connecting autism genetic susceptibility and cellular and circuit alterations in the human brain. This data is the raw differential gene expression comparing ASD versus CTL subjects for each cell cluster.

opencc-zeroJan 2024View details →

Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids

Abstract: Disruptions in the tightly regulated process of human brain development have been linked to increased risk for brain and mental illnesses. While the genetic contribution to these diseases is well established, important environmental factors have been less studied at molecular and cellular levels. In this study, we used single-cell and cell-type-specific techniques to investigate the effect of glucocorticoid (GC) exposure, a mediator of antenatal environmental risk, on gene regulation and lineage specification in unguided human neural organoids. We characterized the transcriptional response to chronic GC exposure during neural differentiation and studied the underlying gene regulatory networks by integrating single-cell transcriptomics- with chromatin accessibility data. We found lasting cell type-specific changes that included autism risk genes and several transcription factors associated with neurodevelopment. Chronic GCs influenced lineage specification primarily by priming the inhibitory neuron lineage through key transcription factors like PBX3. We provide evidence for convergence of genetic and environmental risk factors through a common mechanism of altering lineage specification.