Find research datasets worth reusing

Diatom cell-size composition as a novel tool for quantitative estimates of water table in peatlands

Diatom cell-size composition is an indicator of aquatic environmental changes, but has been rarely investigated, especially in semi-terrestrial peatlands. In this study, both taxonomic composition and cell-size composition of diatoms were analyzed in 41 samples from two montane peatlands, northeastern China. Redundancy analyses revealed that diatom taxonomic composition was significantly related to the depth to the water table (DWT) and Ca2+, while cell-size composition was significantly associated with DWT and Si. DWT was the most important factor and its sole effect explained 26.2% and 17.9% of the total variance in taxonomic composition and cell-size composition, respectively. Accordingly, diatom-based water-table transfer functions were developed based on taxonomic composition and cell-size composition, respectively. The maximum likelihood (ML) model based on diatom taxonomic composition had the best performance, with the correlation coefficient value (R2) of 0.78 and the root mean squared error of prediction (RMSEP) of 6.66 cm. The ML model based on cell-size composition had similar performance, with the R2 of 0.78 and the RMSEP of 6.87cm, suggesting that diatom cell-size composition can be a new quantitative means to track past water-table changes.

The role of Cornulin (CRNN) in the progression of cutaneous squamous cell carcinoma involving AKT activation in SCL-1

Cutaneous squamous cell carcinoma (cSCC) is a prevalent type of skin cancer that has been on the rise in recent times, particularly among older individuals. Cornulin (CRNN) is increasingly recognized as an oncogene involved in developing various types of tumors. However, the precise contribution to cSCC remains unclear. Our study observed a significant increase in CRNN expression in cSCC samples compared to healthy skin. CRNN expression in the SCL-1 cell line derived from cSCC was reduced, leading to a halt in cell growth during the transition from the G1 phase to the S phase. This reduction inhibits cell division, promotes cell death, and decreases cell invasion and migration. CRNN overexpression has been found to enhance cell growth and prevent cells from undergoing natural cell death, and the cancer-promoting effects of CRNN are linked to AKT activation. Using a mouse xenograft model, we demonstrated that the inhibition of CRNN led to a decline in cSCC tumor growth in a living organism, providing evidence of CRNN’s involvement in cSCC occurrence and development. This study establishes a foundation for evaluating the effectiveness of CRNN in treating cSCC, enabling further investigation in this area

Single-cell transcriptomic profiling of human pancreatic islets reveals genes responsive to glucose exposure over 24 hours

Aims/hypothesis: Disruption of pancreatic islet function and glucose homeostasis can lead to the development of sustained hyperglycemia, beta cell glucotoxicity, and subsequently type 2 diabetes. In this study, we explored the effects of in vitro hyperglycemic conditions on human pancreatic islet gene expression across 24 hours in six pancreatic cell types: alpha, beta, gamma, delta, ductal, and acinar cells. We hypothesized that genes associated with hyperglycemic conditions may be relevant to the onset and progression of diabetes. Methods: We exposed human pancreatic islets from two donors to low (2.8 mmol/l) and high (15.0 mmol/l) glucose concentrations over 24 hours in vitro. To assess the transcriptome, we performed single-cell RNA sequencing (scRNA-seq) at seven time points. We modeled time as both a discrete and continuous variable to determine momentary and longitudinal changes in transcription associated with islet time in culture or glucose exposure. Additionally, we integrated genomic features and genetic summary statistics to nominate candidate effector genes. For three of these genes, we functionally characterized the effect on insulin production and secretion using CRISPR interference to knockdown gene expression in EndoC-βH1 cells, followed by a glucose-stimulated insulin secretion assay. Results: Across all cell types, we identified 1,447 genes associated with time, 680 genes associated with glucose exposure, and 418 genes associated with interaction effects between time and glucose. By integrating these expression profiles with summary statistics from genetic association studies, we identified 2,449 candidate effector genes for type 2 diabetes, HbA1c, random blood glucose, and fasting blood glucose. Of these candidate effector genes, we showed that three—ERO1B, HNRNPA2B1, and RHOBTB3—exhibited an effect on glucose-stimulated insulin secretion and production in EndoC-βH1 cells. Conclusions/interpretation: The findings of our study provide an in-depth characterization of the 24-hour transcriptomic response of human pancreatic islets to glucose exposure at a single-cell resolution. By integrating differentially expressed genes with genetic signals for type 2 diabetes and glucose-related traits, we provide insights into the molecular mechanisms underlying glucose homeostasis. Finally, we provide functional evidence to support the role of three candidate effector genes in insulin secretion and production.

opencc-by-4.0Jun 2023View details →

A risk-reward examination of sample multiplexing reagents for Single Cell RNA-Seq

<div> <h2>A Risk-reward Examination of Sample Multiplexing Reagents for Single Cell RNA-Seq</h2> <div>The publication is available open access at https://doi.org/10.1016/j.ygeno.2024.110793</div> </div> Be sure to check the md5 checksum: checklist.chk

Unveiling the autoreactome: Proteome-wide immunological fingerprints reveal the promise of plasma cell depleting therapy

The prevalence and burden of autoimmune and autoantibody mediated disease continues to rise, yet the etiologies of many of these diseases remain unclear. Despite numerous new targeted immunomodulatory therapies, comprehensive approaches to apply and evaluate the effects of these treatments longitudinally are lacking. Here, we leverage advances in PhIPseq methodology to explore the modulation, or lack thereof, for autoreactive antibodies proteome-wide in both health and disease. We demonstrate that each individual, regardless of disease state, possesses a distinct set of autoreactivities constituting a unique immunological fingerprint, or "autoreactome", that is remarkably stable over years. In addition to uncovering important new biology, the autoreactome can be used to better evaluate the relative effectiveness of various therapies in altering autoantibody repertoires. We find that therapies targeting B-Cell Maturation Antigen (BCMA) profoundly alter an individual's autoreactome, while anti-CD19 and CD-20 therapies have minimal effects, strongly suggesting a rationale for BCMA or other plasma cell targeted therapies in autoantibody mediated diseases.

From hidden hearing loss to supranormal auditory processing by neurotrophin 3-mediated modulation of inner hair cell synapse density

Loss of synapses between spiral ganglion neurons and inner hair cells (IHC synaptopathy), leads to an auditory neuropathy called hidden hearing loss (HHL) characterized by normal auditory thresholds but reduced amplitude of sound-evoked auditory potentials. It has been proposed that synaptopathy and HHL result in poor performance in challenging hearing tasks despite a normal audiogram. However, this has only been tested in animals after exposure to noise or ototoxic drugs, which can cause deficits beyond synaptopathy. Furthermore, the impact of supernumerary synapses on auditory processing has not been evaluated. Here, we studied mice in which IHC synapse counts were increased or decreased by altering neurotrophin 3 (Ntf3) expression in IHC-supporting cells. As we previously showed, postnatal Ntf3 knockdown or overexpression reduces or increases, respectively, IHC synapse density and suprathreshold amplitude of sound-evoked auditory potentials without changing cochlear thresholds. We now show that IHC synapse density does not influence the magnitude of the acoustic startle reflex or its prepulse inhibition. In contrast, gap-prepulse inhibition, a behavioral test for auditory temporal processing, is reduced or enhanced according to Ntf3 expression levels. These results indicate that IHC synaptopathy causes temporal processing deficits predicted in HHL. Furthermore, the improvement in temporal acuity achieved by increasing Ntf3 expression and synapse density suggests a therapeutic strategy for improving hearing in noise for individuals with synaptopathy of various etiologies.

opencc-by-4.0Feb 2024View details →

Dataset: Phytoplankton Cell-States: multiparameter lifetime flow monitoring reveals cellular heterogeneity

<h1>Dataset for Multiparameter-based photosynthetic state transitions of single phytoplankton cells data.</h1> <h2>Creating environment</h2> yaml and spec file are provided of the conda environment used. Most packages are typical, with the key exception of fretbursts A custom/development version of fretbursts was used, which contains support for more flexible photon selection (Ph_sel) objects, necessary for the larger parameter space. This version is in the polarization branch of harripd fork of fretbursts. The simple route to install is  <code>pip install git+https://https://github.com/harripd/FRETBursts@polarization</code> however, if you want to ensure the exact same version is installed use: <code>pip install git+https://github.com/harripd/FRETBursts@12a5168</code> <h2>Data organization</h2> All zip files are meant to be unziped into the same destination folder (ie if a file is in a folder in the zip file, it should be in a subfolder inside the shared highest level folder, but if two files inside different zip folders are in the root of their respective zip files, they should be places in the same folder when all files are unzipped. After unzipping everything your folder for this article should contain the following items (normal text indicates file, bold text indicates folder). <ol> <li>Flow_PhytoCellStates_figures.ipynb</li> <li>mpAlgae</li> <li>figures</li> <li>20230905_cyanoWH8102_diurnal</li> <li>20230707_cyanolightjump</li> <li>20230609_ppurp</li> <li>20230724_redalgaelightjump</li> <li>20231211_pmicans_6umol_diurnal</li> <li>20231217_pmicans_6umol_lightjump</li> <li>20231019_WH8102_imaging</li> <li>bulk_cyano_lightjump</li> <li>synWH8102_di_REPO_20230905.hdf5</li> <li>synWH8102_di_REPO_20230905.csv</li> <li>synWH8102_lj_REPO_20230707.hdf5</li> <li>synWH8102_lj_REPO_20230707.csv</li> <li>ppurp_di_REPO_20230609.hdf5</li> <li>ppurp_di_REPO_20230609.csv</li> <li>ppurp_lj_REPO_20230724.hdf5</li> <li>ppurp_lj_REPO_20230724.csv</li> <li>pmicans_di_REPO_20231211.hdf5</li> <li>pmicans_di_REPO_20231211.csv</li> <li>ppurp_lj_REPO_20230724.hdf5</li> <li>ppurp_lj_REPO_20230724.csv</li> </ol> Flow_API_all.ipynb (item 1) is the jupyter notebook that analyses the data and produces the figures. It relies on having mpAlgae (item 2) in the same folder, as it contains the underlying code that adapts FRETBurts to work with the cell based data, adding functionality to combine multiple data files into one experiment, dynamic gating of data, storing calculated values to disk, which also reduces the memory requirements of the system, as well as a number of advanced plotting functions. Flow_API_all.ipynb also expects a figures folder (item 3) to exist so that it can save the produced figures. It also expects items 4-9 to exist, as those folder names are recorded as where the different raw data sets are stored. Even numbered items 12-22 (all items 12-23 that are hdf5 files) are produced by Flow_API_all.ipynb, and are where processed values of burst search are stored. the mpAlgae api makes it so that if these files are present, burst search is skipped, and instead loaded from these result files. Thus if you desire to examine the data, you only need the top level hdf5 files. These files also save results of histogram fittings, so that results can be loaded instead of recalculatd.  The csv files are export of calculated parameters to csv format. Note that these are ungated, and thus proper gating must be implemented if plots are to be recapitulated from these files, this is done so that alternative gating strategies can also be explored.

Optical coherence tomography of the macular ganglion cell layer in children with neurofibromatosis type 1 is a useful tool in the assessment for optic pathway gliomas

To investigate whether the ganglion cell layer assessed by OCT is a reliable measure to identify and detect relapses of symptomatic OPGs in children with NF1.

Automated cell annotation in scRNA-seq data using unique marker gene sets

Single-cell RNA sequencing has revolutionized the study of cellular heterogeneity, yet accurate cell type annotation remains a significant challenge. Inconsistent labels, technological variability, and limitations in transferring annotations from reference datasets hinder precise annotation. This study presents a novel approach for accurate cell type annotation in scRNA-seq data using unique marker gene sets. By manually curating cell type names and markers from 280 publications, we verified marker expression profiles across these datasets and unified nomenclatures to consistently identify 166 cell types and subtypes. Our customized algorithm, which builds on the AUCell method, achieves accurate cell labeling at single-cell resolution and surpasses the performance of reference-based tools like Azimuth, especially in distinguishing closely related subtypes. To enhance accessibility and practical utility for researchers, we have also developed a user-friendly application that automates the cell typing process, enabling efficient verification and supporting comprehensive downstream analyses. The desktop application can be accessed at <a href="https://omnibusx.com/">https://omnibusx.com</a>.

opencc-by-4.0Jan 2023View details →

Cell type matching across species using protein embeddings and transfer learning

TACTiCS is a method to transfer and align cell types in cross-species data. This repository contains the protein sequences, protein embeddings, count matrices and trained models for human, mouse and marmoset.

Payload-delivering engineered γδ T cells display enhanced cytotoxicity, persistence, and efficacy in preclinical models of osteosarcoma

T cell-based cancer immunotherapy has typically relied on membrane-bound cytotoxicity enhancers such as chimeric antigen receptors expressed in autologous αβ T cells. These approaches are limited by tonic signaling of synthetic constructs and costs associated with manufacturing. γδ T cells are an emerging alternative for cellular therapy, possessing innate anti-tumor activity, potent antibody-dependent cellular cytotoxicity, and minimal alloreactivity. We present an immunotherapeutic platform technology built around the innate properties of the Vγ9Vδ2 T cell, harnessing specific characteristics of this cell type and offering an allo-compatible cellular therapy that recruits bystander immunity. We engineered γδ T cells to secrete synthetic tumor-targeting opsonins in the form of an scFv-Fc fusion protein and a mitogenic IL-15Ra–IL-15 fusion protein (stIL15). Using GD2 as a model antigen, we show that GD2-specific opsonin-secreting Vγ9Vδ2 T cells (stIL15-OPS-γδ T cells) have enhanced cytotoxicity and promote bystander activity of other lymphoid and myeloid cells. Secretion of stIL-15 abrogated the need for exogenous cytokine supplementation and further mediated activation of bystander natural killer cells. Compared to unmodified γδ T cells, stIL15-OPS-γδ T cells exhibited superior in vivo control of subcutaneous tumors and persistence in the blood. Moreover, stIL15-OPS-γδ T cells were efficacious against patient-derived osteosarcomas in animal models and in vitro, where efficacy could be boosted with the addition of zoledronic acid. Together the data identify stIL15-OPS-γδ T cells as a candidate allogeneic cell therapy platform combining direct cytolysis with bystander activation to promote tumor control.

opencc-by-4.0Apr 2024View details →

Remotely controlled 3D-engineered scaffolds for biomimetic in vitro investigations on brain cell co-cultures

Open the record for dataset details and reuse information.

Datasets accompanying "Deciphering the heterogeneity of differentiating hPSC-derived corneal limbal stem cells through single-cell RNA-sequencing"

Datasets include two seurat objects: one with all unfiltered cells and raw expression data (seu_unfiltered.rds) and one dataset with normalised expression and latest annotations (differentiation_object_latest.rds). Additionally, a single-cell object containing post-(py)SCENIC analysis is added (ipsc_scenic.h5ad).

Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 10

Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container. Data set 10 comprises an image series of 255 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the T1 detector of the SEM at high vacuum. Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.

Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 05

Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container. Data set 05 comprises an image series of 500 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 6 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.

Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 03

Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container. Data set 03 comprises an image 3D model of a Giardia lamblia cell adhered to the plastic substrate of a culture dish. The model was generated by segmentation of the entire cell, the cell nuclei (red) and the ventral disc cytoskeleton (yellow) in an image series of 276 images which was recorded by SBF SEM (see dataset 01). Section interval was 50 nm and pixel size 10 nm. The data folder contains the model-file (Imaris-format) and a 360° rotation of the model as video file (mp4-format).

Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 02

Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container. Data set 02 comprises an image series of 1462 images recorded of a Giardia lamblia cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.5 mbar). Original pixel size was 5 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.

Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 09

Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container. Data set 09 comprises an image series of 400 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.

Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 08

Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container. Data set 08 comprises an image series of 299 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 3 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.

Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 04

Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container. Data set 04 comprises an image series of 120 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the T1 detector of the SEM at high vacuum. Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.