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opencc-zeroSep 2020View details →

Data from: The effects of body mass on immune cell concentrations of mammals

Theory predicts that body mass should affect the way organisms evolve and use immune defenses. We investigated the relationship between body mass and blood neutrophil and lymphocyte concentrations among 250+ terrestrial mammalian species. We tested whether existing theories (e.g., Protecton Theory, immune system complexity, and rate of metabolism) accurately predicted the scaling of immune cell concentrations. We also evaluated the predictive power of body mass for these leukocyte concentrations compared to sociality, diet, life history, and phylogenetic relatedness. Phylogeny explained >65% of variation in both lymphocytes and neutrophils, and body mass appeared more informative than other interspecific trait variation. In the best-fit mass-only model, neutrophils scaled hypermetrically (b = 0.11) with body mass whereas lymphocytes scaled isometrically. Extrapolating to total cell numbers, this exponent means that an African elephant circulates 13.3 million times the neutrophils of a house mouse, whereas their masses differ by only 250k-fold. We hypothesize that such high neutrophil numbers might offset the i) higher overall parasite exposure that large animals face and/or ii) the higher relative replication capacities of pathogens to host cells.

opencc-by-4.0Oct 2020View details →

Production and purification of receptor-binding domain (RBD) of the Spike protein from a transiently transfected mammalian cell

Production and purification of recombinant receptor-binding domain (RBD) of the Spike protein from a transiently transfected EXPI293 mammalian cell .

opencc-zeroOct 2020View details →

During hippocampal inactivation, grid cells maintain synchrony, even when the grid pattern is lost

The grid cell network in the medial entorhinal cortex (MEC) has been subject to thorough testing and analysis, and many theories for their formation have been suggested. To test some of these theories, we re-analyzed data from Bonnevie et al., 2013, in which the hippocampus was inactivated and grid cells were recorded in the rat MEC. We investigated whether the firing associations of grid cells depend on hippocampal inputs. Specifically, we examined temporal and spatial correlations in the firing times of simultaneously recorded grid cells before and during hippocampal inactivation. Our analysis revealed evidence of network coherence in grid cells even in the absence of hippocampal input to the MEC, both in regular grid cells and in those that became head-direction cells after hippocampal inactivation. This favors models, which suggest that phase relations between grid cells in the MEC are dependent on intrinsic connectivity within the MEC.

opencc-zeroNov 2020View details →

Identification of an inhibitory neuron subtype, the L-stellate cells of the cochlear nucleus

Auditory processing depends upon inhibitory signaling by interneurons, even at its earliest stages in the ventral cochlear nucleus (VCN). Remarkably, to date only a single subtype of inhibitory neuron has been documented in the VCN, a projection neuron termed the D-stellate cell. With the use of a transgenic mouse line, optical clearing and imaging techniques, combined with electrophysiological tools, we revealed a population of glycinergic cells in the VCN distinct from the D-stellate cell. These novel multipolar glycinergic cells were smaller in soma size and dendritic area, but over 10-fold more numerous than D-stellate cells. They were activated by auditory nerve fibers and T-stellate cells, and made local inhibitory synaptic contacts on principal cells of the VCN. Given their abundance, combined with their narrow dendritic fields and axonal projections, it is likely that these neurons, here termed L-stellate cells, play a significant role in frequency-specific processing of acoustic signals.

Recognized trophoblast-like cells conversion from human embryonic stem cells by BMP4 based on convolutional neural network

The use of models of stem cell differentiation to trophoblastic cells provides an effective perspective for understanding the early molecular events in the establishment and maintenance of human pregnancy. In combination with the newly developed deep learning technology, the automated identification of this process can greatly accelerate the contribution to relevant knowledge. Based on the transfer learning technique, we used a convolutional neural network to distinguish the microscopic images of Embryonic stem cells (ESCs) from differentiated trophoblasts -like cells (TBL). To tackle the problem of insufficient training data, the strategies of data augmentation were used. The results showed that the convolutional neural network could successfully recognize trophoblast cells and stem cells automatically, but could not distinguish TBL from the immortalized trophoblast cell lines in vitro (JEG-3 and HTR8-SVneo). We compare the recognition effect of the commonly used convolutional neural network, including DenseNet, VGG16, VGG19, InceptionV3, and Xception. This study extends the deep learning technique to trophoblast cell phenotype classification and paves the way for automatic bright-field microscopic image analysis of trophoblast cells in the future.

Single-cell repertoire and transcriptome sequencing reveals clonally expanded and transcriptionally distinct lymphocytes in aged CNS

Single-cell repertoire and transcriptome sequencing reveals clonally expanded and transcriptionally distinct lymphocytes in aged CNS. Gene expression and immune receptor repertoire sequencing was performing for both B and T cells. This dataset contains the VDJ sequencing information for the four samples. Each B cell and T cell library was sequenced across four lanes.    Files with _WT_ in their name correspond to the young (4-6 week B6 mice)  Files with _12_ in their name before the BDJ or VDJ text correspond to the 12-month-old cohort. Files with _18_ in their name before the BDJ or VDJ text correspond to the 18-month-old cohort in which four brains were pooled. Files with 4_18_ in their name before the BDJ or VDJ text correspond to the 18-month-old mouse that was processed and sequenced alone.    The L001 - L004 in the file names indicates the sequencing lane. Samples with BDJ correspond to the B cell repertoire library (B cell VDJ). Samples with TDJ correspond to the T cell repertoire library (T cell VDJ).

Single-cell immune repertoire sequencing of two convalescent COVID-19 patients

Single-cell immune repertoire sequencing of two convalescent COVID-19 patients using 10x genomics 5' immune profiling. Resulting output files are from the count and vdj functions from 10x genomic's cellranger v3.1.0.

Characterization of photorecruitable Guanine Exchange Factors for the study of Rho GTPases in endothelial cells

Time lapses of respective figures belonging to the report titled "Characterization of photorecruitable Guanine Exchange Factors for the study of Rho GTPases in endothelial cells". This report was written as part of the Msc programe in Biomedical Science of the University of Amsterdam.

opencc-by-4.0Jul 2020View details →

ChIP-seq of plasma cell-free nucleosomes identifies cell-of-origin gene expression programs

Genomic DNA is packed by histone proteins that carry a multitude of post-translational modifications  that reflect cellular transcriptional state. Cell-free DNA (cfDNA) is derived from fragmented chromatin in dying cells, and as such it retains the histones markings present in the cells of origin. Here, we pioneer chromatin immunoprecipitation followed by sequencing of cell-free nucleosomes (cfChIP-seq) carrying active chromatin marks. Our results show that cfChIP-seq provides multidimensional epigenetic information that recapitulates the epigenetic and transcriptional landscape in the cells of origin. We applied cfChIP-seq to 268 samples including samples from patients with heart and liver pathologies, and 135 samples from 56 metastatic CRC patients. We show that cfChIP-seq can detect pathology-related transcriptional changes at the site of the disease, beyond the information on tissue of origin. In CRC patients we detect clinically-relevant, and patient-specific information, including transcriptionally active HER2 amplifications. cfChIP-seq provides genome-wide information and requires low sequencing depth. Altogether, we establish cell-free chromatin immunoprecipitation as an exciting modality with potential for diagnosis and interrogation of physiological and pathological processes using a simple blood test.

The Clinical Significance of Serum p53 Antibody Levels in Patients with Oral Squamous Cell Carcinoma in Japanese Clinical Practice

Supplementary Figure S1. Serum anti-p53 antibody titers in each clinical stage. Supplementary Table S1. The change of Ap53Ab titer in patients  with OSCC after surgery.

Fiji/CellProfiler cell migration timelapse data set and code

This zenodo upload consists of: Fiji IJMacro script create_LabelledMasks.ijm CellProfiler pipeline TrackMate_CellProfiler.cppipe Matlab script Plot_per_cell.m  Saved manually curated TrackMate project crop_1_60_ManualCuration.xml Saved Spots Results Table of manually curated TrackMate project: Spots in tracks statistics.csv CellProfiler pipeline output cp_output.zip Example data set crop_1_60.tif - subset of image data previously described in: <a href="https://www.zotero.org/google-docs/?9YEDuq">Shafqat-Abbasi, H., Kowalewski, J. M., Kiss, A., Gong, X., Hernandez-Varas, P., Berge, U., Jafari-Mamaghani, M., Lock, J. G., and Strömblad, S. 2016. An analysis toolbox to explore mesenchymal migration heterogeneity reveals adaptive switching between distinct modes. eLife 5:e11384–e11384.</a> Many thanks to Staffan Strömblad et al. for sharing the data.

opencc-zeroDec 2020View details →

Data from: Are acute and acclimated thermal effects on metabolic rate modulated by cell size? A comparison between diploid and triploid zebrafish larvae

Being composed of small cells may carry energetic costs related to maintaining ionic gradients across cell membranes as well as benefits related to diffusive oxygen uptake. Here we test the hypothesis that these costs and benefits of cell size in ectotherms are temperature dependent. To study the consequences of cell size for whole-organism metabolic rate we compared diploid and triploid zebrafish larvae differing in cell size. A fully factorial design was applied combining three different rearing and test temperatures that allowed us to distinguish acute from acclimated thermal effects. Individual oxygen consumption rates of diploid and triploid larvae across declining levels of oxygen availability were measured. We found that both acute and acclimated thermal effects affected the metabolic response. In comparison to triploids, diploids responded more strongly to acute temperatures, especially when reared at the highest temperature. These observations support the hypothesis that animals composed of smaller cells (i.e. diploids) are less vulnerable to oxygen limitation in warm aquatic habitats. Furthermore, we found slightly improved hypoxia tolerance in diploids. By contrast, warm-reared triploids had higher metabolic rates when they were tested at acute cold temperature, suggesting that being composed of larger cells may provide metabolic advantages in the cold. We offer two mechanisms as a potential explanation of this result, related to homeoviscous adaptation of membrane function and the mitigation of developmental noise. Our results suggest that being composed of larger cells provides metabolic advantages in cold water, while being composed of smaller cells provides metabolic advantages in warm water.

Data sets comparing Ca(2+) dynamics in whole-cell and β-escin-based perforated patch clamp recordings in adult mouse brain slices.

# Hess-et-al-beta-escin-2020 Data of the "Data in Brief" article concerning the added buffer approach with beta-escin perforated patch. A joint work by: Simon Hess (`simon.hess@uni-koeln.de`), Christophe Pouzat (`christophe.pouzat@math.unistra.fr`), and Peter Kloppenburg (`peter.kloppenburg@uni-koeln.de`). ## Content This repository contains: - Directory `data_whole_cell` contains the experimental data in [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) format. The data contains recordings of _Substantia nigra_ dopaminergic neurons recorded in the whole-cell configuration. - Directory `data_beta_escin` contains the experimental data in [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) format. The data contains recordings of _Substantia nigra_ dopaminergic neurons recorded in the β-escin perforated patch clamp configuration.

Labeling and tracking of immune cells in ex vivo human skin

Example imaging datasets linked to the publication 'Labeling and tracking of immune cells in ex vivo human skin' (doi: 10.1038/s41596-020-00435-8). Additional information filenames: - m = ex vivo murine skin - h = ex vivo human skin - mCD8= anti-murine CD8-AF594 nanobody staining (red) - hCD8= anti-human CD8-AF594 nanobody staining (red) - Hoechst= Hoechst 33342 staining (grey) - CD1a= anti-hCD1a-AF488 staining (green) - CD103= anti-hCD103-AF488 staining (green) - SHG = second harmonic generation (cyan) Imaris x64 v9.2.0.

Effects of trabectedin in the zebrafish Danio rerio: from cells to larvae

These archives contain the original data set for the research article "Effects of trabectedin in the zebrafish Danio rerio: from cells to larvae"   FACS_ZFL_cells_Trabectedin.rar  Contains the original data regarding cells morphology evaluated by flow cytometry (Becton Dickinson FACScan). Original data set_ This archive contains the original data tables for the research article "Effects of trabectedin in the zebrafish Danio rerio: from cells to larvae" Original data set_Spreadsheet Trypan Blue test_in vitro Cells viability on ZFL exposed to trabectedin measured by Trypan blue dye exclusion method Original data set_Spreadsheet MTT test_in vitro Cytotoxicity of trabectedin and doxorubicin (positive control) against ZFL cells as analyzed by the MTT assay Original data set_Spreadsheet Survival_in vivo Percentage of zebrafish embryos under trabectedin exposure Original data set_Spreadsheet Abnormalities_in vivo Percentage of abnormalities (somite alteration, pericardial edema, tail malformations, lack of equilibrium) of zebrafish embryos under trabectedin exposure Original data set_Spreadsheet Swimming behavior_in vivo Total distance covered and mean velocity by zebrafish larvae (120 hpf) after exposure to trabectedin

AhR Gene Expression in Immune cell subtypes

Benjamin J. Schmiedel, Divya Singh, Ariel Madrigal, Alan G. Valdovino-Gonzalez, Brandie M. White, Jose Zapardiel-Gonzalo, Brendan Ha, Gokmen Altay, Jason A. Greenbaum, Graham McVicker, Grégory Seumois, Anjana Rao, Mitchell Kronenberg, Bjoern Peters, Pandurangan Vijayanand, Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression, Cell, Volume 175, Issue 6, 2018, Pages 1701-1715.e16, ISSN 0092-8674, https://doi.org/10.1016/j.cell.2018.10.022. (http://www.sciencedirect.com/science/article/pii/S009286741831331X) Abstract: Summary While many genetic variants have been associated with risk for human diseases, how these variants affect gene expression in various cell types remains largely unknown. To address this gap, the DICE (database of immune cell expression, expression quantitative trait loci [eQTLs], and epigenomics) project was established. Considering all human immune cell types and conditions studied, we identified cis-eQTLs for a total of 12,254 unique genes, which represent 61% of all protein-coding genes expressed in these cell types. Strikingly, a large fraction (41%) of these genes showed a strong cis-association with genotype only in a single cell type. We also found that biological sex is associated with major differences in immune cell gene expression in a highly cell-specific manner. These datasets will help reveal the effects of disease risk-associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis (https://dice-database.org). Keywords: DICE; immunology; GWAS; genetic variants; human immune cells; gene expression; eGenes; eQTLs; sex https://dice-database.org/genes/ahr#boxplot

opencc-zeroJan 2021View details →

Data from: Multi-omics analyses on rheumatoid arthritis in CD4+ T cells

Objective: CD4+ T cells have been suggested as the most disease-relevant cell type in rheumatoid arthritis (RA) in which RA-risk non-coding variants exhibit allele-specific effects on regulation of RA-driving genes. This study aimed to understand RA-specific signatures in CD4+ T cells using multi-omics data, interpreting inter-omics relationships in shaping the RA transcriptomic landscape. Methods: We profiled genome-wide variants, gene expression, and DNA methylation in CD4+ T cells from 82 RA patients and 40 healthy controls using high-throughput technologies. We investigated differentially expressed genes (DEGs) and differentially methylated regions (DMRs) in RA and localized quantitative trait loci (QTLs) for expression and methylation. We then integrated these based on individual-level correlations to inspect DEG-regulating sources and investigated the potential regulatory roles of RA-risk variants by a partitioned-heritability enrichment analysis with RA genome-wide association summary statistics. Results: A large number of RA-specific DEGs were identified (n=2,575), highlighting T-cell differentiation and activation pathways. RA-specific DMRs, preferentially located in T-cell regulatory regions, were correlated with the expression levels of 548 DEGs mostly in the same topologically associating domains. In addition, expressional variances in 771 and 83 DEGs were partially explained by expression QTLs for DEGs and methylation QTLs for DEG-correlated DMRs, respectively. A large number of RA variants were moderately to strongly correlated with meQTLs. DEG-correlated DMRs, enriched with meQTLs, had strongly enriched heritability of RA. Conclusion: Our findings revealed that the methylomic changes, driven by RA heritability-explaining variants, shape the differential expression of a substantial fraction of DEGs in CD4+ T cells in RA patients, reinforcing the importance of a multi-dimensional approach in disease-relevant tissues.

Super-resolved Reflectance Confocal Microscopy data on Diatom shells and live MEF cells

This dataset is linked to a paper submission in Open Research Europe. It contains the RAW data of confocal reflectance super-resolved point spread function, diatom shell zstack and time lapse imaging of a living Mouse Embryonic Fibroblast cell.

Super-resolved Reflectance Confocal Microscopy time-lapse imaging of a living MEF cell lamellipod

This movies presents a time-lapse of a label-free living Mouse embryonic fibroblast cell observed with super-resolved rescanned reflectance confocal microscopy..

Particle-in-cell Simulation of the Neutrino Fast Flavor Instability

1D_fiducial.tgz contains the input parameters and simulation output data from the fiducial simulation. Each timestamp with output data is stored in a plt* directory. scripts.tgz contains the data reduction and plotting scripts used in the paper. We require yt to read the data with our scripts. inputs.tgz contains input files for each of the simulations in the paper. The test problem inputs (MSW, bipolar, homogeneous FFI, inhomogeneous FFI) are part of the test suite in Emu. Simulations are run using the version of Emu (v1.1) at http://doi.org/10.5281/zenodo.4423166 or https://github.com/AMReX-Astro/Emu.