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111,247 results for “cells”
Single-Cell RNA-Sequencing Reveals Placental Response under Environmental Stress
<p>This repository provides scRNA-seq data corresponding to the manuscript "Single-Cell RNA-Sequencing Reveals Placental Response under Environmental Stress" by Van Buren, Azzara, Rangel-Moreno, de la Luz Garcia-Hernandez, Murphy, Cohen, Lin, and Park. The repository includes both count by gene matrices output from CellRanger version 6.0.1 (file names *_filtered_feature_matrix.h5 for each of the eight samples Control_1_M, Control_1_F, Control_2_M, Control_2_F, As_1_M, As_1_F, As_2_M, As_2_F), and a finalized Seurat object including cell type assignments as used for analyses in the manuscript (file name final_Seurat_obj.RData). Accompanying code used in analysis can be found at https://github.com/edvanburen/placenta_code.</p>
A potential patient stratification biomarker for Parkinson´s disease based on LRRK2 kinase-mediated centrosomal alterations in peripheral blood-derived cells
<p>Annotated WES VCF file and phenotype file used in Gene burden analysis of Naaldijk et al., "A potential patient stratification biomarker for Parkinson´s disease based on LRRK2 kinase-mediated centrosomal alterations in peripheral blood-derived cells", 2023. </p><p> </p>
Gleaning Euglenozoa-specific DNA polymerases in public single-cell transcriptome data
<p><span>Multiple genes encoding family A DNA polymerases (famA DNAPs), which are evolutionary relatives of DNA polymerase </span><span>I</span><span> (Pol</span><span>I</span><span>) in bacteria and phages, have been found in eukaryotic genomes, and many of these proteins are used mainly in organelles. Among members of the phylum Euglenozoa, distinct types of famA DNAP, Pol</span><span>I</span><span>A, Pol</span><span>I</span><span>BCD+, POP, and eugPolA, have been found. It is intriguing how the suite of famA DNAPs had been established during the evolution of Euglenozoa, but the DNAP data have not been sampled from the taxa that sufficiently represent the diversity of this phylum. In particular, little sequence data were available for basal branching species in Euglenozoa until recently. Thanks to the single-cell transcriptome data from symbiontids and phagotrophic euglenids, we have an opportunity to cover the "hole" in the repertory of famA DNAPs in the deep branches in Euglenozoa. The current study identified 16 new famA DNAP sequences in the transcriptome data from 33 phagotrophic euglenids and two symbiontids, respectively. Based on the new famA DNAP sequences, the updated diversity and evolution of famA DNAPs in Euglenozoa are discussed.</span></p>
Data from: Effect of stretching on inflammation in a subcutaneous carrageenan mouse model analyzed at single-cell resolution
<p>Understanding the factors that influence the biological response to inflammation is crucial, due to its involvement in physiological and pathological processes, including tissue repair/healing, cancer, infections, and autoimmune diseases. We have previously demonstrated that in vivo stretching can reduce inflammation and increase local pro-resolving lipid mediators in rats, suggesting a direct mechanical effect on inflammation resolution. Here, we aimed to explore further the effects of stretching at the cellular/molecular level in a mouse subcutaneous carrageenan-inflammation model. Stretching for 10 minutes twice a day reduced inflammation, increased the production of pro-resolving mediator pathway intermediate 17-HDHA at 48h post carrageenan injection, and decreased both pro-resolving and pro-inflammatory mediators (e.g., PGE<sub>2</sub> and PGD<sub>2</sub>) at 96h. ScRNAseq analysis of inflammatory lesions at 96h showed that stretching increased the expression of both pro-inflammatory (<em>Nos2</em>) and pro-resolution (<em>Arg1</em>) genes in M1 and M2 macrophages at 96 hours. An intercellular communication analysis predicted specific ligand-receptor interactions orchestrated by neutrophils and M2a macrophages, suggesting a continuous neutrophil presence recruiting immune cells such as activated macrophages to contain the antigen while promoting resolution and preserving tissue homeostasis.</p>
Dataset for "Effect of benzothiadiazole-based π-spacers on fine-tuning of optoelectronic properties of oligothiophene-core donor materials for efficient organic solar cells: a DFT study"
<p># Data and code for "Effect of benzothiadiazole-based π-spacers on fine-tuning of optoelectronic properties of oligothiophene-core donor materials for efficient organic solar cells: a DFT study."</p><p>## Contents</p><p>* data-{type}/*: reproducible data</p><p>* job.job : example slurm script</p><p> </p><p>## Description of the data</p><p>The data are organized in subdirectories *data-{type}/{system}/* corresponding to the considered molecules and simulation type:</p><p>* data-gs: Ground state calculations</p><p>* data-td: TD-DFT calculations</p><p>The contents of each subdirectory are:</p><p>* data-gs/{system}/structure.xyz: physical atomic structure</p><p>* data-td/{system}/td-dft/td_uvvis.txt: photoabsorption spectrum</p><p>The spectrum plots in the article correspond to the first (x values) and second (y values) columns of the spectrum files.</p><p> </p><p>## Reproduction of the data</p><p>The data were produced using Gaussian version g16.A.01</p><p>The calculation of the data of a system consists of the following steps:</p><p>1. Ground-state (gs) calculation:</p><p> * Prepare the input file for the gs by adjusting the parameters of the ground state calculations:</p><p> * "# opt b3lyp/6-311+g(d,p) scrf=(smd,solvent=chloroform) geom=connectivity empiricaldispersion=gd3bj out=wfn"</p><p> * out = wfn keyword to create a wfn file of the ground state that will be used for EDD and RDG investigations</p><p> * Submit the job.job file for the gs calculation as appropriate for the particular input file of the system</p><p> * The optimized sturctures are visualised using GaussView</p><p>2. Time-propagation calculation:</p><p> * Requires finished ground-state calculation</p><p> * Set up the TD-DFT calculation parameters as necessary:</p><p> * "# td=(nstates=6) wb97xd/6-311+g(d,p) scrf=(smd,solvent=chloroform) guess=read density out=wfn"</p><p> * density out = wfn keywords to create a wfn file of the excited state that will be used for EDD investigation</p><p> * Submit the job.job file for TD-DFT calculation as appropriate for the particular system</p><p> * The photoabsoption specta are visualised using GaussView</p><p>3. RDG calculation:</p><p> * Put the .wfn file of the gs calculation in the command window of the open source Multiwfn software and follow the sturcture in Section 3.23.1 in the manual</p><p>4. DOS calculation:</p><p> * The dos curves are plotted starting from the .fchk of the ground state geometry, select the atoms index corresponding to the diffrents subpart of the studied molecules (donor, acceptor, pi-spacer)</p><p> * Put the .fchk file of the gs calculation in the command window of the open source Multiwfn software and follow the structure in Section 4.10.1 in the manual</p><p> * the output generates .chk file which is transformed to .fchk file : formchk .chk .fch</p><p>5. TDM calculations:</p><p> * Requires finished ground-state calculation</p><p> * Set up the TD-DFT calculaton parameters as necessary</p><p> * "# td=(nstates=6) wb97xd/6-311+g(d,p) scrf=(smd,solvent=chloroform) guess=read density transition=1 iop(6/8=3) out=wfn"</p><p> * Put the .fchk file of the gs calculation in the command window of the open source Multiwfn software and follow the sturcture in Section 4.18.8 in the manual</p><p>6. EDD calculation:</p><p> * Edd plots are plotted based on the es.wfn and gs.wfn following Section 4.18.1 in the manual</p><p> </p>
Oxygen concentration profiles data and code from: Langet et al., 2023, Single-celled bioturbators: benthic foraminifera mediate oxygen penetration and prokaryotic diversity in intertidal sediment
<p>This archive contains the data of measured oxygen profile and the scripts used to generate the oxygen surface fluxes for the article</p><p>Langlet, D., Mermillod-Blondin, F., Deldicq, N., Bauville, A., Duong, G., Konecny, L., Hugoni, M., Denis, L., and Bouchet, V. M. P.: Single-celled bioturbators: benthic foraminifera mediate oxygen penetration and prokaryotic diversity in intertidal sediment, Biogeosciences, 20, 4875–4891, https://doi.org/10.5194/bg-20-4875-2023, 2023.</p>
Aneuploid embryonic stem cells drive teratoma metastasis: source data
<h3>The dataset of "<strong>Aneuploid embryonic stem cells drive teratoma metastasis</strong>"</h3><p>1. Pathway enrichment of scRNA-seq.csv: a table containing the pathway enrichment results. (<strong>Supplementary fig10 d</strong>)</p><p>2. Bulk_RNA_processed.RDS: a Seurat object containing the results of bulk RNA-seq. (<strong>Supplementary fig11 h-l</strong>)</p><p>3. Relative cell abundance of ES captured by scRNA-seq.csv: A table containing the relative abundance of ES sub-populations in all ES cells for each sample. (<strong>fig5 c</strong>)</p><p>4. WES_out.RDS: an R object containing the results of WES processed by maftools. (<strong>fig2 b-g</strong>)</p><p>5. bulk_RNA_raw_matrix.RDS: an R object containing the raw count matrix of bulk RNA-seq samples. (<strong>Supplementary fig11 h-l</strong>)</p><p>6. scRNA-seq DEGs -- ES_stem vs. ES_Ori(WT).csv: a table containing the results of DEG analysis. (<strong>fig5 f</strong>)</p><p>7. scRNA-seq DEGs -- ES_stem vs. ES_Ori(AC).csv: a table containing the results of DEG analysis. (<strong>fig5 f</strong>)</p><p>8. pseudo time DEGs of scRNA-seq.csv: DEGs that change as ES differentiation. (<strong>fig5 e</strong>)</p><p>9. scRNA-seq_meta_info.tsv.gz: the meta information of scRNA-seq data. (<strong>fig5 and Supplementary fig10</strong>)</p><p>10. scRNA-seq_raw_matrix.mtx.gz: the raw count matrix of scRNA-seq data. (<strong>fig5 and Supplementary fig10</strong>)</p>
Cell thicknesses calculated for the tripolar grid used by the GREP reanalyses
<p>Cell thicknesses were calculated for the tripolar NEMO0.25 grid used by the GREP reanalyses (ORAS5, CGLORS, GLORYS2V4, FOAM).</p>
Multimodal Epigenetic Sequencing Analysis (MESA) of Cell-free DNA for Non-invasive Colorectal Cancer Detection
<p>Processed data (feature-by-sample matrices) of non-disruptive bisulfite-free methylation sequencing for cfDNA samples from 4 clinical cohorts (Cohort 1, Cohort 2, Cohort 3, and cfTAPS dataset). Codes used to repeat the results in our paper can be found https://rpubs.com/LiYumei/926228 and https://github.com/ChaorongC/MESA. </p>
High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species
<p>With populations of threatened and endangered species declining worldwide, efforts are being made to generate high-quality genomic records of these species before they are lost forever. Here, we demonstrate that data from single Oxford Nanopore Technologies (ONT) MinION flow cells can, even in the absence of highly accurate short DNA-read polishing, produce high-quality <em>de novo</em> plant genome assemblies adequate for downstream analyses, such as synteny and ploidy evaluations, paleodemographic analyses, and phylogenomics. This study focuses on three North American ash tree species in the genus <em>Fraxinus</em> (Oleaceae) that were recently added to the International Union for Conservation of Nature (IUCN) Red List as critically endangered. Our results support a whole genome triplication at the base of the Oleaceae as well as a subsequent whole genome duplication shared by <em>Syringa</em>, <em>Osmanthus</em>, <em>Olea, and Fraxinus</em>. Finally, we demonstrate the use of ONT long-read sequencing data to reveal patterns in demographic history.</p>
Exploring Cellular Dynamics: A Comprehensive Analysis of SH-SY5Y Cell Growth in Variable Polycarbonate Chambers and Comparative Insights with Standard Petri Dishes
<div> <div> <div> <div> <div> <div> <p>The provided illustrations delineate the proliferation of SH-SY5Y cells within polycarbonate chambers with varying diameters, ranging from 3 mm to 50 mm. HBE and HeLaGFP cells serve as points of comparison. Five microscopic images were captured for each culture plate, one at the central location and four at random sites. To trace the growth trajectory across different chamber sizes, images from various culture days underwent manual binarization using GIMP and/or ImageJ software. The resulting binarized images can be accessed in the 'masks' directories within the zipped files, corresponding to the attached images. Comparative analysis of cell growth within these chambers was conducted against growth observed in standard 60 mm Petri dishes from Corning.</p> <p>For monitoring cell growth, we employed an Olympus phase-contrast microscope (CKX53) equipped with a DLT camera (DLT-Cam PRO 1080 HDMI USB).</p> <div> <div> <div> <p>The file nomenclature employed herein serves to represent the primary experimental conditions under consideration. It comprises a hierarchical structure, encompassing various parameters as follows: cellsName_passageNumber_cellSuspension_measurementDayNumber_chamberDiameter_regionNumber_hOfFluids_number.</p> <p>The cellsNames parameter encapsulates the complete nomenclature of the cells utilized in the experiment.</p> <p>The passageNumber parameter represents the passage number and is encoded as 'pNumber.'</p> <p>The cellSuspension parameter is denoted by distinct codes:</p> <ul> <li>'c1' designates a cell suspension with a concentration of 5x10^5 cells/ml.</li> <li>'c3' signifies a cell suspension with a concentration of 1x10^5 cells/ml.</li> <li>'c4' denotes a cell suspension with a concentration of 5x10^4 cells/ml.</li> </ul> <p>The measurementDayNumber parameter is encoded as 'afterXXXdays,' signifying the number of culture days.</p> <p>The 'd' followed by a number (e.g., d6, d8, d10, d12, d15) indicates the diameter of the chamber in millimeters. In a given series of files (e.g., 1day_d6_1, 1day_d6_2, 1day_d6_3, 1day_d6_4, 1day_d6_5), the trailing numeral (_1, _2, _3, _4, _5) corresponds to a photograph captured in a distinct region of the sample.</p> <p>The hOfFluids parameter is employed to signify the height ('h') of the fluid above the cells in the chamber, expressed in millimeters.</p> <div> <div> <div> <p>In adherence to the aforementioned conventions, every file name serves to distinctly characterize a particular collection of experimental conditions. This practice enhances both the comprehensibility and systematic organization of the data. It is noteworthy that the complete set of parameters may not always be provided; for instance, the height of the column of medium is assumed to be 2 mm unless otherwise specified.</p> </div> </div> </div> </div> </div> </div> <br> <p> </p> </div> </div> </div> </div> </div> </div>
Single-Stranded DNA with Internal Base Modifications Mediates Highly Efficient Gene Insertion in Primary Cells
<p>The manuscript describes the use of ssDNA with chemical modifications in internal bases to improve gene insertion. The dataset contains an excel file with the data corresponding to the figures in this manuscript. In addition, it has results from next-generation sequencing used in Figure 2B. </p>
Real-time influence of intracellular acidification and Na+/H+ exchanger inhibition on in-cell pyruvate metabolism in the perfused mouse heart: A 31P-NMR and hyperpolarized 13C-NMR study
<p>This dataset contains primary data for DOI: 10.1002/nbm.4993</p> <p>NMR in Biomedicine. 2023; 10;e4993</p> <p>Title: Real-time influence of intracellular acidification and Na+/H+ exchanger inhibition on in-cell pyruvate metabolism in the perfused mouse heart: A 31P-NMR and hyperpolarized 13C-NMR study</p> <p>Authors: David Shaul, Naama Lev-Cohain, Gal Sapir, Jacob Sosna, J. Moshe Gomori, Leo Joskowicz, Rachel Katz-Brull</p> <p> </p> <p>Description:</p> <p>These primary datasets contains data presented in the above publication and consist of 31P- (at thermal equilibrium) and hyperpolarized 13C-NMR spectra. </p> <p>Please consult the Archive Guide.</p>
Multi-omics analysis of innate and adaptive responses to BCG vaccination reveals epigenetic cell states that predict trained immunity
<p>This repository contains personal immune profiles of 323 healthy individuals (300BCG) subjected to Bacillus Calmette-Guérin (BCG) with blood samples collected immediately before (day 0), and 14 and 90 days after the vaccination. The personal immune profiles comprise:</p> <ul> <li>immune cell concentrations measured with flow cytometry and a hematology analyzer</li> <li>plasma concentrations of 73 circulating inflammatory markers</li> <li>30 measurements of cytokine and lactate production capacity of peripheral blood mononuclear cells (PBMCs) in response to four microbial stimuli (Candida albicans, Escherichia coli lipopolysaccharide [LPS], Staphylococcus aureus, Mycobacterium tuberculosis).</li> </ul> <p>Visit <a href="http://300BCG.bocklab.org/">http://300BCG.bocklab.org/</a> to learn more.</p>
Xrp1 ChIP-seq database (data from Xrp1 is a transcription factor required for cell competition-driven elimination of loser cells)
<p>Xrp1 ChIP-seq data from Baillon et al. 2018, "Xrp1 is a transcription factor required for cell competition-driven elimination of loser cells".</p>
Kopflose Statue auf dem Hehlentorfriedhof Celle
**beschädigte Statue auf dem ehemaligen Hehlentorfriedhof in Celle | Damaged, headless statue at the former Hehlentor cemetery in Celle** Statue auf dem ehemaligen Hehlentorfriedhof, nördlich der Aller im Zentrum Celles gelegen. Der Friedhof wurde im 16. Jahrhundert gegründet und ist seit 1979 öffentliche Grünanlage der Stadt. Weitere Informationen: | Further information at [www.celle.de](https://www.celle.de/Celle-entdecken/Friedh%C3%B6fe/Hehlentorfriedhof.php?object=tx,2727.5&ModID=7&FID=2092.601.1&NavID=2727.66&La=1) Aufnahmen von | captured by Marvin, Ayad, Eline & Lucie (25.03.2022) zusätzliche Aufnahmen | additional capturing by Pl (26.03.2022) Dank an | Thanks [kulturschokolade.org](https://sketchfab.com/3dtwins) für das gemeinsame Projekt! Source: Objaverse 1.0 / Sketchfab
Eiserne Glocke der Stadtkirche St. Marien Celle
**Ehemalige eiserne Uhrschlagglocke der Celler Stadtkirche St. Marien von 1918 | Former iron bell at St. Marien Church, Celle** Diese Glocke von 1918 ist ungefähr 90 cm hoch und 80 cm breit und steht in der Kalandgasse an der Stadtkirche St. Marien in Celle. Sie diente im damals neu errichteten Kirchturm von 1918 bis 2008 als Uhrschlagglocke. Weitere Informationen: | Further information at [www.stadtkirche-celle.de](https://www.stadtkirche-celle.de/bauwerk/stadtkirche_st_marien/glocken) Aufnahmen von | captured by Milad, Aimée, Florine & Nazif (25.03.2022) Dank an | Thanks [kulturschokolade.org](https://sketchfab.com/3dtwins) für das gemeinsame Projekt! Source: Objaverse 1.0 / Sketchfab
A Model of a model of the City of Celle
one of the lesser known but most iconic German Cities in lower Saxony. Untouched by war for centuries, the city center of Celle consists of a huge number of half-timbered houses ranging back to at least 1526. Celle has a beautiful castle, and the old church stands in a center of a city thats blueprint has been unchanged for centuries. Source: Objaverse 1.0 / Sketchfab
Double Twin Cell
The various methods of expansion of the covered dwelling area, according to the progressive 'doubling', both in height and in depth, have determined the so-called 'typological process': from the 'matrix' type of elementary cells to the single-family row house or terrace-house type, up to the recent multi-family in-line house type (present sporadically in Pienza and only for the 'recast' of terraced houses). Single-cell homes, especially during the 19th century, expanded in height with the addition of a third floor, or merged together giving rise to online associations, to one or two apartments per floor. The stairs that connect the floors together are generally located in a central position. Although today the survey of the number of floors shows that most of the buildings consists of three floors above ground, probably the same houses originally did not exceed two floors. [Learn More](https://esg.pt/3dpast/platform/pienza/multiple-cells.html) Source: Objaverse 1.0 / Sketchfab
Statue am St. Josef-Stift Celle
**Statue am ehemaligen Krankenhaus St. Josef-Stift in Celle | Statue at former St. Josef-Stift hospital in Celle** Die Statue mit einem Heiligenbildnis befindet sich am Gebäude des 1883 errichteten katholischen St. Josef-Stifts, eines ehemaligen Krankenhauses in der Innenstadt von Celle. Aufnahmen von | captured by Charlotte, Piet, Paul & Mika (25.03.2022) Dank an | Thanks [kulturschokolade.org](https://sketchfab.com/3dtwins) für das gemeinsame Projekt! Source: Objaverse 1.0 / Sketchfab
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.