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7,459 results for “kidney”
Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbAA kidneys injected or not with heme
<p>The objective of this experiment was to explore the <span>transcriptome</span> of the <span>HbSS Townes</span> <span>mouse model</span> of <span>sickle cell disease</span>.Townes model mice carry several human hemoglobin <span>knock-in</span> genes replacing the endogenous mouse genes and may be useful in studying <span>sickle cell disease</span>.All mice were <span>genotyped</span>, age- and sex-matched littermates. All <span>HbAA</span> (control, normal human hemoglobin) vs HbSS (<span>sickle cell disease</span>, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group <span>heterogeneity</span>. <span>Hemin</span> (<span>Ferriprotoporphyrin IX</span>) was purchased from <span>Frontiers Scientific</span> and injected <span>intravenously</span> (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received <span>PBS</span> instead. Mice were anesthetized with <span>isoflurane</span> 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection.</p> <p>The results of kidney (indicated rein) from HbAA mice injected or not with <span>heme</span> are presented here . </p> <p>The results of kidney (indicated rein) from HbSS mice injected or not with <span>heme</span> can be found at number </p> <p>Thirty μm-thick frozen tissue sections of kidneys were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit <span>Promega</span> AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all <span>Agilent Technologies</span>, <span>Palo Alto, CA</span>, <span>USA</span>). RNA Integrity Numbers superior to 7 were eligible for subsequent <span>reverse transcription</span> into <span>cDNA</span>. <span>RNAseq</span> was performed at the GenomIC plateform <span>Cochin</span> Institute INSERM U1016. After <span>RNA extraction</span>, RNA quality (<span>RNA integrity number</span>) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (<span>Illumina</span>) according to manufacturer instructions. Briefly, purified <span>poly-A</span> containing mRNA molecules were fragmented and <span>reverse-transcribed</span> using random <span>primers</span>. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the <span>cDNA</span> was followed by <span>ligation</span> of <span>Illumina</span> adapters.<br>Libraries were quantified by <span>qPCR</span> using <span>KAPA Library Quantification</span> Kits for <span>Illumina</span> Libraries (KapaBiosystems, <span>Wilmington</span>, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an <span>Agilent</span> Bioanalyzer. Libraries were sequenced on an <span>Illumina</span> Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a <span>paired-end</span> mode. After sequencing, primary analysis based on AOZAN software (ENS, <span>Paris</span>), was applied to <span>demultiplex</span> and control the quality of the <span>raw data</span> (based of FastQC modules / version 0.11.5).</p> <p>The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA <span>PBS</span>, HbAA <span>heme</span>, HbSS <span>PBS</span>, <span>HbSS</span> <span>heme</span>. </p>
The molecular architecture of the kidney slit diaphragm revealed by cryo-electron tomography
<p>Data supporting the article :</p> <p><strong>The molecular architecture of the kidney slit diaphragm revealed by cryo-electron tomography</strong></p> <p><em>Alexandra N. Birtasu, Konstantin Wieland, Serena M. Arghittu, Utz H. Ermel, Maciej K Kocylowski, Margot P. Scheffer, Bernd Fakler, Roberto Covino, Florian Grahammer, Achilleas S. Frangakis</em></p>
Regulatory T cell therapy is associated with distinct immune regulatory lymphocytic infiltrates in kidney transplants: Spatial transcriptomic dataset and images
<p>The outputs of the NanoString GeoMx DSP platform were concatenated into three xlsx files, each illustrating a separate experiment along with their sample annotations. This technique analyzes protein or RNA abundance within regions of interest (ROIs) or specific cell segments selected based on histological features and immunofluorescence. In this repository, the concatenated GeoMx output files are presented, along with PowerPoint presentations for each biopsy that show immunofluorescence images of the selected ROIs and/or cell segments.</p> <ul> <li><strong>Protein_Full ROI:</strong> This experiment measured the abundance of 41 proteins in discrete regions of interest (ROIs) within transplant kidney biopsies.</li> <li><strong>Protein_Rare cell:</strong> This experiment measured the abundance of 40 proteins in specific cell segments, such as CD4+FoxP3- cells vs. CD4+FoxP3+ cells, within transplant kidney biopsies.</li> <li><strong>RNA:</strong> This experiment measured the abundance of 90 genes in discrete ROIs within transplant kidney biopsies.</li> </ul>
Characterizing Metabolic Alterations in Early-stage chronic kidney disease (CKD) patients: A Pathway for Improved Diagnosis and Personalized Treatment.
<p>The raw NMR data that I have uploaded contains the final concentration results that have been used for this study.</p>
Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci
<p>Trans-ethnic meta-analysis results for eGFR EWAS</p> <p>Description of variables:</p> <p>CpG CPG name<br> chr Chromosome <br> pos_hg38 Position hg38 <br> Beta Effect <br> SE Standard error <br> P P value <br> totalsamplesize number of participants <br> direction direction of effect for studies <br> hetpval P value for heterogeneity <br> hetdf Degree of freedom <br> gene Gene location</p> <p>Upload of this dataset was completed by The EWAS Catalog team. The data can be queried along with hundreds of other EWAS at ewascatalog.org. To upload your EWAS summary statistics and have a zenodo DOI generated for you go to ewascatalog.org/upload. </p>
Dataset related to article "Amnion epithelial cells are an effective source of factor H and prevent kidney complement deposition in factor H deficient mice"
<p>File excel with raw data of parameters (column) for any single animal (line) of each experimental group</p>
KPMP Datasets for a Reference Tissue Atlas for the Human Kidney
<p>This is the dataset for the publication of A Reference Tissue Atlas for the Human Kidney from the Kidney Precision Medicine Project (KPMP). KPMP is building a spatially-specified human kidney tissue atlas in health and disease with single-cell resolution. Here, we describe the construction of an integrated reference map of cells, pathways and genes using unaffected regions of nephrectomy tissues and undiseased human biopsies from 56 subjects. We use single-cell/nucleus transcriptomics, subsegmental laser-microdissection transcriptomics and proteomics, near-single-cell proteomics, 3-D and CODEX imaging, and spatial metabolomics to hierarchically identify genes, pathways and cells. Integrated data from these different technologies coherently identify cell types/subtypes within different nephron segments and the interstitium. These profiles describe cell-level functional organization of the kidney following its physiological functions and link cell subtypes to genes, proteins, metabolites and pathways. They further show that mRNA levels along the nephron are congruent with the subsegmental physiological activity. This reference atlas provides a framework for classification of kidney disease when multiple molecular mechanisms underlie convergent clinical phenotypes.</p>
Lipidomic data of the kidney cortex from diabetic mice fed MUFA-HFD and SFA-HFD
<p><span>In diabetic patients, </span><span>dyslipidemia </span><span>frequently contributes to organ damage such as </span><span>diabetic kidney disease (DKD). DKD is associated with excessive renal deposition of triacylglycerol (TAG) in lipid droplets (LD). Yet, it is unclear whether LDs play a protective or damaging role and how this might be influenced by dietary patterns. By using a diabetes mouse model, we find here that high-fat diet enriched in the unsaturated oleic acid (OA) caused more lipid storage in LDs in renal proximal tubular cells (PTC) but less tubular damage than a corresponding butter diet with the saturated palmitic acid (PA). In order to study the changes in the lipidome, we performed shotgun lipidomics on the kidney cortex of these mice.</span></p>
Processed data for MethylBoostER: an XGBoost model to classify kidney cancer subtypes
<p>This is a repository containing processed data for MethylBoostER, an XGBoost model that classifies kidney cancer subtypes. The open-source code can be found here: https://github.com/ss-lab-cancerunit/MethylBoostER.</p>
Kidney transplantation waiting times and risk of cardiovascular events and mortality: a retrospective observational cohort study in Taiwan
<p>Objectives: Patients with end-stage renal disease (ESRD) are at a high risk of cardiovascular events (CVEs), and kidney transplantation (KT) has been reported to improve risk of CVEs and survival. As the association of KT timing on long-term survival and clinical outcomes remains unclear, we investigated the association of different KT waiting times on clinical outcomes.</p> <p>Design: Retrospective observational cohort study.</p> <p>Setting: We conducted an observational cohort study using data from the National Health Insurance Research Database in Taiwan. Adult patients who initiated kidney transplantation therapy from 1997 to 2013 were included.</p> <p>Participants: A total of 3562 adult patients who initiated uncomplicated KT therapy were included and categorized into four groups according to KT waiting times after ESRD: Group 1 (<1 year), Group 2 (1–3 years), Group 3 (3–6 years), and Group 4 (>6 years).</p> <p>Primary outcome measure: The main outcome was a composite of all-cause death, nonfatal myocardial infarction, or nonfatal stroke, based on the primary diagnosis in medical records during hospitalization.</p> <p>Results: Compared with Group 1, the adjusted risk of primary outcome events (all-cause death, nonfatal myocardial infarction, or nonfatal stroke) increased by 1.67 times in Group 2 (95% CI: 1.40–2.00; P <0.001), 2.17 times in Group 3 (95% CI: 1.73–2.71; P <0.001), and 3.10 times in Group 4 (95% CI: 2.21–4.35; P <0.001). The rates of primary outcome events were 6.7%, 13.4%, and 14.0% within five years, increasing to 19.5%, 26.3%, and 30.8% within 10 years in Groups 1, 2, and 3, respectively.</p> <p>Conclusions: Our results demonstrate that early KT is associated with superior long-term cardiovascular outcomes compared to late KT in selected ESRD patients receiving uncomplicated KT, suggesting that an early KT could be a better treatment option for ESRD patients who are eligible for transplantation.</p>
Other supporting data for our manuscript "Mapping the Single Cell Transcriptomic Response of Murine Diabetic Kidney Disease to Therapies"
<p>Other supplementary data for our paper "Mapping the Single Cell Transcriptomic Response of Murine Diabetic Kidney Disease to Therapies"</p>
KidDO progress presentation 2022: Metabolic Targets for Therapeutic Intervention in Kidney Disease
<p>This is a recorded talk with head of the KidDO project - Robert Fenton - where he presents the latest project progress.</p> <p>The talk was given at one of ODIN's (the Open Discovery Innovation Network) Knowledge Sharing Events in May 2022.</p> <p> </p> <p> </p>
Extended zenodo data figures for, "An atlas of healthy and injured cell states and niches in the human kidney"
<p>This repository includes extended data zenodo figures for the manuscript, "An atlas of healthy and injured cell states and niches in the human kidney." Figures and figure legends are included in the included pdf file.</p>
Supporting data and analysis for, "An atlas of healthy and injured cell states and niches in the human kidney"
<p>Online repository for contents associated with kidney cell state atlas: </p> <p>This combines the image datasets used for the manuscript describing an approach for the integrated tissue cytometry analysis of mesoscale confocal imaging datasets.</p> <p>Linked deposits:</p> <table> <tbody> <tr> <td>Zenodo Extended Data figures</td> <td>10.5281/zenodo.7120908</td> </tr> <tr> <td>3D Cytometry and neighborhood analysis</td> <td>10.5281/zenodo.7120941</td> </tr> <tr> <td>Github repository, "Cell-State-Atlas_2022"</td> <td>https://github.com/KPMP/Cell-State-Atlas-2022</td> </tr> </tbody> </table> <p> </p> <p> </p>
Merged Adult Human Kidney sc & snRNA-seq dataset
<p>A merged human kidney scRNA-seq dataset made from the following scRNA-seq studies:</p> <p>Lake, B.B. et al. A single-nucleus RNA-sequencing pipeline to decipher the molecular anatomy and pathophysiology of human kidneys. Nat Commun 10, 2832 (2019).</p> <p>Liao, J., Yu, Z., Chen, Y. et al. Single-cell RNA sequencing of human kidney. Sci Data 7, 4 (2020).</p> <p>Menon, R. et al. Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker. JCI Insight 5, e133267 (2020).</p> <p>Wu, H. et al. Single-cell transcriptomics of a human kidney allograft biopsy specimen defines a diverse inflammatory response. J Am Soc Nephrol 29: 2069–2080 (2018).</p> <p>Young, M. D. et al. Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors. Science 361, 594–599 (2018).</p>
CHRONIC KIDNEY DISEASE SCREENING IN COMMUNITY PHARMACY: CRIERFAC PROJECT
<p>Chronic kidney disease (CKD) is a major health problem. Early detection improves the prognosis of these patients, but the disease does not show its face until it is more advanced. The aim is to screen for the disease in community pharmacies in order to refer patients to primary care physicians.</p> <p>Data from the 2116 patients recruited are presented in a single Excel table where each line corresponds to one patient. It contains patient demographics data, risk factors for chronic kidney disease, creatinine and glomerular filtration data, pharmacist intervention and physician response.</p>
Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease
<p>This dataset contains raw and processed seqFISH data quantifying 1300 genes within single cells from three Acute Kidney Injury (AKI) and three control mice kidneys. The dataset also contains the codebook and probe sequences used to create probe libraries for the seqFISH experiments.</p> <p><strong>Supplementary_data_tables</strong> folder contains the supplementary data tables for the manuscript: Data_1 contains DE gene expression, Data_2 and Data_3 contain the codebook and probe sequence information needed to generate the probe libraries used for the seqFISH experiments. Data_4 contains the probe sequence information needed to generate the serial probes against <em>Vcam1</em> and <em>Havcr1</em></p> <p><strong>AKI_Ctrl_object.rds</strong> - Seurat object generated from seqFISH data for the AKI and healthy control mice as detailed in the manuscript.</p> <p><strong>Counts_raw.csv </strong>contains raw gene counts for all cells in the dataset.</p> <p><strong>coordinates.csv</strong> contains the xy coordinates (in um) for every cell in the dataset.</p> <p><strong>metadata.csv</strong> contains the metadata for each cell in the dataset including sample and cell type allocation as well as Microenvironment (ME) assignment. This file also contains expression data of <em>Vcam1</em> and <em>Havcr1, </em>which were detected using serial probes as detailed in the manuscript.</p>
Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease
<p>Kidney injury disrupts the intricate renal architecture and triggers limited regeneration, and injury-invoked inflammation and fibrosis. Deciphering molecular pathways and cellular interactions driving these processes is challenging due to the complex renal architecture. Here, we apply single cell spatial transcriptomics to examine ischemia-reperfusion injury in the mouse kidney. Spatial transcriptomics reveals injury-specific and spatially-dependent gene expression patterns in distinct cellular microenvironments within the kidney and predicts <em>Clcf1-Crfl1</em> in a molecular interplay between persistently injured proximal tubule cells and neighboring fibroblasts. Immune cell types play a critical role in organ repair. Spatial analysis reveals cellular microenvironments resembling early tertiary lymphoid structures and identifies associated molecular pathways. Collectively, this study supports a focus on molecular interactions in cellular microenvironments to enhance understanding of injury, repair and disease.</p>
Analysis results for association study of long-term kidney transplant rejection using whole-exome sequencing
<p>Association study results for long-term kidney transplant rejection. Single-variant association results are provided as Plink output files. Meta-analysis results are provided as METAL output files. FDR results are sorted lists of the top association result from random sample label permutations and are included with the plink and meta-analysis results. SKAT and GSEA results are provided for gene and pathway level analyses, respectively.</p>
Training dataset: MALDI imaging of N-glycans in murine kidney sections
<p>The files provided here are all adopted from the <a href="http://www.ebi.ac.uk/pride/archive/projects/PXD009808">PRIDE PXD009808 datasets</a> and the corresponding publication: Ove J. R. Gustafsson, Matthew T. Briggs, Mark R. Condina, Lyron J. Winderbaum, Matthias Pelzing, Shaun R. McColl, Arun V. Everest-Dass, Nicolle H. Packer, Peter Hoffmann. “MALDI imaging mass spectrometry of N-linked glycans on formalin-fixed paraffin-embedded murine kidney.” Analytical and Bioanalytical Chemistry (2015) 407: 2127. <a href="https://doi.org/10.1007/s00216-014-8293-7">https://doi.org/10.1007/s00216-014-8293-7</a></p> <p><br> Three 6µm sections of formalin-fixed paraffin-embedded murine kidney tissue specimens were prepared for MALDI imaging. To release N-linked glycans, PNGase F was printed onto two kidney sections. In the third section one area was printed with buffer to serve as a control and another area was covered with N-glycan calibrants (Gustafsson et al., Figure 4 a-c). 2,5-DHB matrix was sprayed onto the tissue sections and MALDI imaging was performed with 100 µm spatial resolution using a MALDI-TOF/TOF instrument.</p> <p><br> We processed the original imzML files to make them concise but meaningful as training data sets in the Galaxy training network (https://galaxyproject.github.io/training-material/).<br> We reduced the m/z range to 1250 – 2310 and resampled the m/z values with a step size of 0.1. The main part of the training is based on the control and first treated kidney file for which we selected representative pixels to further decrease file size (files: ‘control’, ‘treated1’). To test the results on the complete dataset we also provide a file in which both treated kidney sections, the control and the calibrant files are combined after decreasing and resampling the m/z range as described above. The combined file was normalized to the total ion current (TIC) (file: ‘all_files’). All processing steps were performed on<a href="http://https://usegalaxy.eu"> https://usegalaxy.eu</a> with the tools ‘MSI filtering’, ‘MSI combine’ and ‘MSI preprocessing’ in version 1.12.1.3).<br> Additionally, the LC-MS/MS results were extracted from table S2 of the publication by Gustafsson et al. and are provided as tabular file to enable the N-glycan identification (file: 'Glycan_IDs').</p>
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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.