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279 results for “mouse kidney”
Two metabolomics data sets (mouse kidney, mouse plasma), generated for the publication Bignon et al., 2023: "Multiomics reveals multilevel control of renal and systemic metabolism by the renal tubular circadian clock".
<p><strong>Publication: </strong>Bignon Y, Wigger L, Ansermet C, Weger BD, Lagarrigue S, Centeno G, Durussel F, Götz L, Ibberson M, Pradervand S, Quadroni M, Weger M, Amati F, Gachon F, Firsov D. Multiomics reveals multilevel control of renal and systemic metabolism by the renal tubular circadian clock. J Clin Invest. 2023 Mar 2:e167133. doi: 10.1172/JCI167133. Epub ahead of print. PMID: 36862511.</p> <p> </p> <p><strong>Abstract: </strong> Circadian rhythmicity in renal function suggests rhythmic adaptations in renal metabolism. To decipher the role of the circadian clock in renal metabolism, we studied diurnal changes in renal metabolic pathways using integrated transcriptomic, proteomic, and metabolomic analysis performed on control mice and mice with inducible deletion of the circadian clock regulator Bmal1 in the renal tubule (cKOt). With this unique resource, we demonstrated that ~30% RNAs, ~20% proteins and ~20% metabolites are rhythmic in kidneys of control mice. Several key metabolic pathways including NAD+ biosynthesis, fatty acid transport, carnitine shuttle,and b-oxidation displayed impairments in kidneys of cKOt, resulting in a perturbed mitochondrial activity. Carnitine reabsorption from the primary urine was one of the most impacted processes with a ~50% reduction in plasma carnitine levels and a parallel systemic decrease in tissues carnitine content. This suggests that the circadian clock in the renal tubule controls both kidney and systemic physiology.</p> <p> </p> <p><strong>This record contains two separate mass-spectrometry metabolomics data sets associated with this study:</strong></p> <ol> <li>Metabolic profile of renal tubules, MS/MS data, Metabolon, Morrisville, NC (N=60)</li> <li>Metabolic profile of blood plasma, MS/MS data, Biocrates, Innsbruck, Austria (N=60)</li> </ol> <p>For each data set, original data as received from the platforms and processed data as used in the data analysis are provided. Preprocessing of kidney data included removal of metabolites with more than 80% missing data values, median normalization, imputation and glog2 transformation. Preprocessing of plasma data included filtering of metabolites with any missing data and log2 transformation. Details of data processing are available in the STAR*methods of the publication.</p> <p> </p> <p><strong>Data sets in other repositories associated with the same study:</strong></p> <p>Additional data sets (transcriptomics, proteomics) pertaining to the same study have been deposited in public repositories:</p> <ul> <li>Gene Expression Omnibus (NCBI GEO), GSE216252</li> <li>PRIDE Archive (EMBL-EBI), PXD036803</li> </ul> <p> </p>
Simultaneous three-dimensional vascular and tubular imaging of whole mouse kidneys with X-ray µCT
<p>µCT dataset of a mouse kidney injected with contrast agent XlinCA and scanned with 3.3 µm voxel size. Detailed sample preparation and image acquisition protocols are published as <a href="https://doi.org/10.1017/S1431927620001725">"Simultaneous three-dimensional vascular and tubular imaging of whole mouse kidneys with X-ray µCT"</a> in <em>Microscopy and Microanalysis</em>.</p> <p>Segmentations of the vascular and tubular lumina along with the renal tissue are provided as masks. The three different segmented features were combined into a single dataset and encoded as different gray values:</p> <p>0: Background<br> 51: Tubules<br> 204: Tissue<br> 255: Blood vessels</p> <p>The Supplemental Video features a computer graphics visualization of the segmented masks. Blood vessel lumina are rendered in red, tissue in transparent blue and tubular lumina in yellow.</p>
Data from: Ablation of Hoxb3os in mouse polycystic kidney disease exacerbates cystogenesis
<p>Autosomal dominant polycystic kidney disease (ADPKD) is a monogenic disorder characterized by the formation of cysts in the kidney and is primarily caused by mutations in two genes, <em>PKD1</em> and <em>PKD2</em>. In this study, we investigated the role of the long noncoding RNA (lncRNA) <em>Hoxb3os</em> in ADPKD by ablating its expression in the mouse. <em>Hoxb3os</em>-null mice were viable and had grossly normal kidney morphology but displayed activation of mTOR/Akt signaling and subsequent increase in kidney cell proliferation. To determine the role of <em>Hoxb3os</em> in cystogenesis, we crossed the <em>Hoxb3os</em>-null mouse to two orthologous <em>Pkd1</em> mouse models: <em>Pkhd1/Cre</em>;<em>Pkd1<sup>F/F</sup></em> (rapid cyst progression) and <em>Pkd1<sup>RC/RC</sup></em> (slow cyst progression). Ablation of <em>Hoxb3os</em> exacerbated cyst growth in both models. To gain insight into the mechanism whereby <em>Hoxb3os</em> inhibition promotes cystogenesis, we performed proteomic analysis of mTOR/Akt pathway between <em>Pkd1</em> single-knockout (SKO) and <em>Pkd1-Hoxb3os</em> double-knockout (DKO) mice. Compared to SKO, DKO mice presented with enhanced levels of total and phosphorylated Rictor. This was accompanied by increased phosphorylation of Akt<sup>Ser473</sup>, a known mTORC2 effector site. Physiologically, kidneys from DKO mice displayed between 40-50% increase in cell proliferation. Results from this study indicated that ablation of <em>Hoxb3os</em> in mouse PKD exacerbated cystogenesis and dysregulated mTORC2.</p>
Implantation of abdominal imaging windows on the mouse kidney
<p>This video describes the surgical process of implanting an abdominal imaging window (AIW) on the kidney of mice. This window can be used for acute or longitudinal imaging. All experiments have been reviewed and approved by the local authorities (Landesdirektion Sachsen).</p> <p>Implantation of chronic abdominal windows allows for microscopical investigation of highly dynamic processes in physiological and pathological circumstances and is generally tolerated well by experimental animals. It enables insights which otherwise could only be obtained using high numbers of experimental animals. The method can be regarded as reduction approach in terms of 3R implementation.</p> <p>This upload contains the full version and is distributed under CC BY-ND 4.0 license to inhibit decontextualized misuse. Please check license terms for usage, especially for remixing/transforming! If you want to remix the material, get in contact with the author.</p>
Metabolic Derangement in Polycystic Kidney Disease Mouse Models Is Ameliorated by Mitochondrial-Targeted Antioxidants
<p>Autosomal dominant polycystic kidney disease (ADPKD) is characterized by progressively enlarging cysts. Here we elucidate the interplay between oxidative stress, mitochondrial dysfunction, and metabolic derangement using two mouse models of PKD1 mutation, PKD1RC/null and PKD1RC/RC. Mouse kidneys with PKD1 mutation have decreased mitochondrial complexes activity. Targeted proteomics analysis shows a significant decrease in proteins involved in the TCA cycle, fatty acid oxidation (FAO), respiratory complexes, and endogenous antioxidants. Overexpressing mitochondrial-targeted catalase (mCAT) using adeno-associated virus reduces mitochondrial ROS, oxidative damage, ameliorates the progression of PKD and partially restores expression of proteins involved in FAO and the TCA cycle. In human ADPKD cells, inducing mitochondrial ROS increased ERK1/2 phosphorylation and decreased AMPK phosphorylation, whereas the converse was observed with increased scavenging of ROS in the mitochondria. Treatment with the mitochondrial protective peptide, SS31, recapitulates the beneficial effects of mCAT, supporting its potential application as a novel therapeutic for ADPKD.</p>
Single cell ATAC-seq Mouse Kidney Data: Chromatin-accessibility estimation from single-cell ATAC data with scOpen
<p>We provide results regarding the bioinformatic analysis of scATAC-seq from mouse UUO kidney at different time points.</p>
MALDI imaging of mouse kidney peptides - test dataset
<p>This imzML test file is concise but meaningful as a training data set in the Galaxy training network (https://galaxyproject.github.io/training-material/).</p> <p>One 6 µm thick section of formalin-fixed paraffin-embedded mouse kidney (from 6 month old, male, C57 black 6 mice) was mounted onto an indium-tin oxide (ITO) glass slide, deparaffinized and subjected to antigen retrieval in citric acid (pH 6, 100°C, 1h). Before and after antigen retrieval the sample was washed with 10mM ammonium bicarbonate buffer. After air drying, four 1 µl spots of Bombesin (0.01 mg/ml) were placed around the tissue to control digestion.<strong> </strong>Trypsin was sprayed onto the tissue with the iMatrix Sprayer and the sample was incubated for 2 h at 50°C in a humid chamber. Internal Calibrants (Angiotensin I, Substance P, [Glu]-Fibrinopeptide B, ACTH 18-39) were mixed with α-Cyano-4-hydroxycinnamic acid (CHCA) matrix and sprayed onto the sample.</p> <p>The sample was measured with the Applied Biosystems/MDS SCIEX 4800 MALDI TOF/TOF™ Analyzer in reflector positive ion mode and a spatial resolution of 150 µm. The acquired Analyze7.5 file was loaded into Cardinal and filtered to reduce file size and decrease analysis time: Filtering was done for m/z values between 1220 and 1625 as well as pixel that represent about half of the kidney and one Bombesin digestion control spot. The data was exported in the common data format imzML.</p> <p> </p>
KidDO project update - quantitative proteomic and metabolomic analysis of five mouse models with chronic kidney disease
<p>Chronic kidney disease (CKD) is one of the most deadly diseases faced by patients and is a major global health and socioeconomic burden.CKD increases cardiovascular morbidity and premature mortality and decreases quality of life. Hypertension (HTN) and type 2 diabetes mellitus (T2DM), which are reaching epidemic levels, are major risk factors for CKD. CKD diagnosis and progression is based on estimated GFR (eGFR) and urinary albumin excretion. However, eGFR only has a predictive value in advanced disease and there is risk of progressive CKD in non-albuminuric individuals. Thus, there is an urgent need for new approaches for early detection of the most “at risk” individuals and identification of CKD signatures to aid in designing novel drugs and preventive measures that could ameliorate progression of CKD.</p> <p>Our overarching goal is to identify metabolites that predict kidney cell phenotypes during CKD and how crosstalk of these metabolites with the proteome drive CKD progression. We will integrate metabolomics and proteomic information from animal models of CKD with human CKD patient biopsies to identify common signatures in the tubulointerstitium that correlate with human pathophysiology.</p> <p>Here we provide quantitative proteomic and metabolomic datasets, as well as plasma and urine electrolyte measurements on five CKD mouse models.</p>
PANDA cell-type-specific networks for S858R and WT mouse kidney
<p>The below files are from the data/results directory of this associated project and include the following:</p> <ul> <li><strong>PANDA networks</strong> : cell-type-specific TF-gene regulatory networks constructed using multi-omic inputs (snRNA-seq, TF-motif, and PPI) for all cell types in S858R and WT kidney tissues (n = 34). All the files included for PANDA networks indicate the condition (heterozygous or control), tissue (kidney) followed by _PANDA.Rdata. (example: pericytes_heterozygouskidneyexpression_PANDA.Rdata)</li> </ul>
Data from: Ablation of Hoxb3os in mouse polycystic kidney disease exacerbates cystogenesis
Open the record for dataset details and reuse information.
Proteinuric chronic kidney disease mouse model RNAseq
<p>RNA seq in renal cortex from proteinuric CKD mouse model</p>
Implantation of abdominal imaging windows on the mouse kidney - short version
<p>This video describes the surgical process of implanting an abdominal imaging window (AIW) on the kidney of mice. This window can be used for acute or longitudinal imaging. All experiments have been reviewed and approved by the local authorities (Landesdirektion Sachsen).</p> <p>Implantation of chronic abdominal windows allows for microscopical investigation of highly dynamic processes in physiological and pathological circumstances and is generally tolerated well by experimental animals. It enables insights which otherwise could only be obtained using high numbers of experimental animals. The method can be regarded as reduction approach in terms of 3R implementation.</p> <p>This upload contains the shortened version and is distributed under CC BY-ND 4.0 license to inhibit decontextualized misuse. Please check license terms for usage, especially for remixing/transforming! If you want to remix the material, get in contact with the author.</p>
Mouse Kidney Atlas (MKA) & MKA-Extended: Single-cell and single-nucleus reference atlases of the mouse kidney
<p>This deposit contains two linked datasets of the mouse kidney:<br><br></p> <h4><strong>1. MKA (Mouse Kidney Atlas)</strong></h4> <p>A comprehensive reference atlas of the healthy adult mouse kidney, generated by integrating approximately <strong>140,000 cells and nuclei</strong> from <strong>59 publicly available single-cell and single-nucleus RNA-sequencing datasets</strong> across <strong>eight independent studies</strong>.<br>The MKA harmonizes annotations through a <strong>hierarchical cell-type model</strong>, enabling robust cross-study comparisons and accurate labeling of novel or rare cell populations.</p> <ul> <li> <p><strong>Original publication:</strong> Novella-Rausell <em>et al.</em>, <em>iScience</em> (2023). <em>“A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery.” </em>DOI: <a target="_new" rel="noopener">10.1016/j.isci.2023.106877</a></p> </li> <li> <p><strong>Format:</strong> <code>AnnData</code> object (~141,401 observations × 3,000 genes)</p> </li> </ul> <h4><strong>2. MKA-Extended</strong></h4> <p>An expanded version of the MKA. This extended atlas incorporates <strong>immune, injury-induced, and polycystic kidney disease–specific</strong> cellular populations, providing a unified reference for <strong>Tangram-based deconvolution</strong> of spatial transcriptomics datasets.</p> <ul> <li><strong>Original publication: </strong>Yasinoglu <em>et al.</em>, <em>JASN</em>, (2025). <em>“Spatial Transcriptomics Reveals Injured Cells, Signature Genes, and Communication Patterns in the Cyst Microenvironment of Polycystic Kidney Disease.” </em>DOI: 10.1681/ASN.0000000894</li> <li> <p><strong>Format:</strong> <code>AnnData</code> object (~303,791 observations × 12,156 genes)</p> </li> </ul>
Data from: Optimizing mouse surgery with online rectal temperature monitoring and preoperative heat supply. Effects on post-ischemic acute kidney injury.
Body temperature affects outcomes of tissue injury. We hypothesized that online body core temperature recording and selective interventions help to standardize peri-interventional temperature control and the reliability of outcomes in experimental renal ischemia reperfusion injury (IRI). We recorded core temperature in up to seven mice in parallel using a Thermes USB recorder and ret-3-iso rectal probes with three different protocols. Setup A: Heating pad during ischemia time; Setup B: Heating pad from incision to wound closure; Setup C: A ventilated heating chamber before surgery and during ischemia time with surgeries performed on a heating pad. Temperature profile recording displayed significant declines upon installing anesthesia. The profile of the baseline experimental setup A revealed that <1 % of the temperature readings were within the target range of 36.5 to 38.5 °C. Setup B and C increased the target range readings to 34.6 ± 28.0 % and 99.3 ± 1.5 %, respectively. Setup C significantly increased S3 tubular necrosis, neutrophil influx, and mRNA expression of kidney injury markers. In addition, using setup C different ischemia times generated a linear correlation with acute tubular necrosis parameters at a low variability, which further correlated with the degree of kidney atrophy 5 weeks after surgery. Changing temperature control setup A to C was equivalent to 10 minutes more ischemia time. We conclude that body temperature drops quickly in mice upon initiating anesthesia. Immediate heat supply, e.g. in a ventilated heating chamber, and online core temperature monitoring can help to standardize and optimize experimental outcomes.
Lipid polyunsaturated fatty acid chains in mouse kidneys were increased within 5 minutes after a single high dose whole body irradiation
<p>figure and table</p>
Data from: Optimizing mouse surgery with online rectal temperature monitoring and preoperative heat supply. Effects on post-ischemic acute kidney injury.
Open the record for dataset details and reuse information.
Rodent Research-3-CASIS: Mouse kidney transcriptomic proteomic and epigenomic data
The Rodent Research-3 (RR-3) mission was sponsored by the pharmaceutical company Eli Lilly and Co. and the Center for the Advancement of Science in Space to study the effectiveness of a potential countermeasure for the loss of muscle and bone mass that occurs during spaceflight. Twenty BALB/c 18-weeks old female mice (ten controls and ten treated) were flown to the ISS and housed in the Rodent Habitat for 39-42 days. Twenty mice of similar age sex and strain were used for ground controls housed in identical hardware and matching ISS environmental conditions. Basal controls were housed in standard vivarium cages. Spaceflight ground controls and basal groups had blood collected then were euthanized had one hind limb removed and finally whole carcasses were stored at -80 C until dissection. All mice in this data set received only the control/sham injection.
Rodent Research-1 (RR1) NASA Validation Flight: Mouse kidney transcriptomic proteomic and epigenomic data
NASA s Rodent Research (RR) project is playing a critical role in advancing biomedical research on the physiological effects of space environments. Due to the limited resources for conducting biological experiments aboard the International Space Station (ISS) it is imperative to use crew time efficiently while maximizing high-quality science return. NASA s GeneLab project has as its primary objectives to 1) further increase the value of these experiments using a multi-omics systems biology-based approach and 2) disseminate these data without restrictions to the scientific community. The current investigation assessed viability of RNA DNA and protein extracted from archived RR-1 tissue samples for epigenomic transcriptomic and proteomic assays. During the first RR spaceflight experiment a variety of tissue types were harvested from subjects snap-frozen or RNAlater-preserved and then stored at least a year at -80C after return to Earth. They were then prioritized for this investigation based on likelihood of significant scientific value for spaceflight research. All tissues were made available to GeneLab through the bio-specimen sharing program managed by the Ames Life Science Data Archive and included mouse adrenal glands quadriceps gastrocnemius tibialis anterior extensor digitorum longus soleus eye and kidney. We report here protocols for and results of these tissue extractions and thus the feasibility and value of these kinds of omics analyses. In addition to providing additional opportunities for investigation of spaceflight effects on the mouse transcriptome and proteome in new kinds of tissues our results may also be of value to program managers for the prioritization of ISS crew time for rodent research activities.
Analysis of mouse antigen specific germinal centre B cell subset gene signatures in presence and absence of kidney disease during T dependent immunization
GEO Series GSE237445. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
Mouse embryonic kidneys (E13.5): HDAC inhibitor (HDACi) treated vs. Control
GEO Series GSE19581. Mus musculus. 6 samples. Type: Expression profiling by array.
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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.