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Dataset results
1,544 results for “microenvironment”
PRKCI regulates tumor microenvironment through YAP1
GEO Series GSE57258. Homo sapiens. 16 samples. Type: Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing.
CD45+ single cell transcriptomes in the MC38 tumor microenvironment
GEO Series GSE234875. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Multi-inlet spheroid generator for modeling immune microenvironment of glioblastoma (GBM)
GEO Series GSE271170. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
ScRNA-Seq of Human MDS and AML Bone Marrow Marrow Microenvironment.
GEO Series GSE288862. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
Single-cell Multi-omics Analysis of Human Testicular Germ Cell Tumor Reveals its Molecular Features and Microenvironment II
GEO Series GSE229823. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
Dataset related to article "Contrast Administration Impacts CT-Based Radiomics of Colorectal Liver Metastases and Non-Tumoral Liver Parenchyma Revealing the "Radiological" Tumour Microenvironment"
<p>This record contains raw data related to article "Contrast Administration Impacts CT-Based Radiomics of Colorectal Liver Metastases and Non-Tumoral Liver Parenchyma Revealing the "Radiological" Tumour Microenvironment"</p> <p> </p> <p>The impact of the contrast medium on the radiomic textural features (TF) extracted from the CT scan is unclear. We investigated the modification of TFs of colorectal liver metastases (CLM), peritumoral tissue, and liver parenchyma. One hundred and sixty-two patients with 409 CLMs undergoing resection (2017-2020) into a single institution were considered. We analyzed the following volumes of interest (VOIs): The CLM (Tumor-VOI); a 5-mm parenchyma rim around the CLM (Margin-VOI); and a 2-mL sample of parenchyma distant from CLM (Liver-VOI). Forty-five TFs were extracted from each VOI (LIFEx<sup>®®</sup>). Contrast enhancement affected most TFs of the Tumor-VOI (71%) and Margin-VOI (62%), and part of those of the Liver-VOI (44%, <em>p</em> = 0.010). After contrast administration, entropy increased and energy decreased in the Tumor-VOI (0.93 ± 0.10 vs. 0.85 ± 0.14 in pre-contrast; 0.14 ± 0.03 vs. 0.18 ± 0.04, <em>p</em> < 0.001) and Margin-VOI (0.89 ± 0.11 vs. 0.85 ± 0.12; 0.16 ± 0.04 vs. 0.18 ± 0.04, <em>p</em> < 0.001), while remaining stable in the Liver-VOI. Comparing the VOIs, pre-contrast Tumor and Margin-VOI had similar entropy and energy (0.85/0.18 for both), while Liver-VOI had lower values (0.76/0.21, <em>p</em> < 0.001). In the portal phase, a gradient was observed (entropy: Tumor > Margin > Liver; energy: Tumor < Margin < Liver, <em>p</em> < 0.001). Contrast enhancement affected TFs of CLM, while it did not modify entropy and energy of parenchyma. TFs of the peritumoral tissue had modifications similar to the Tumor-VOI despite its radiological aspect being equal to non-tumoral parenchyma.</p>
Dataset to submitted manuscript "Imaging Fluorescence Blinking of a Mitochondrial Localization Probe – a Strategy Combining Site-Specificity with Multi-Parametric Sensing of Cellular Microenvironments"
<p><strong>This folder contains all raw data underlying the results presented in a manuscript, submitted to <em>Small</em></strong><strong>, and entitled:</strong></p> <p> </p> <p><strong><em>Imaging Fluorescence Blinking of a Mitochondrial Localization Probe – a Strategy Combining Site-Specificity with Multi-Parametric Sensing of Cellular Microenvironments</em></strong></p> <p> </p> <p><strong>Authored by:</strong></p> <p>Zhixue Du<sup>a</sup><em>, </em>Joachim Piguet<sup>a,+</sup>, Gleb Baryshnikov<sup>b,+</sup>, Johan Tornmalm<sup>a</sup>, Baris Demirbay<sup>a</sup>, Hans Ågren<sup>b</sup>, Jerker Widengren<sup>a,*</sup></p> <p> </p> <p><sup>a</sup> Royal Institute of Technology (KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova Univ Center 106 91 Stockholm, Sweden</p> <p><sup>b</sup> Royal Institute of Technology (KTH), Dept Theroretical Chemistry and Biology, Albanova Univ Center 106 91 Stockholm, Sweden</p> <p><sup>+</sup> Contributed equally</p> <p>* Corresponding author: Email: <a href="mailto:jwideng@kth.se">jwideng@kth.se</a>, Phone: +46-8-7907813</p> <p> </p> <p><strong>The data files are grouped into the different techniques used to generate them, and refer to the figures/tables in the manuscript where the extracted results are presented. </strong></p> <p> </p> <p><strong>ABSTRACT</strong></p> <p>The local microenvironment of mitochondrial membranes directly influences cellular metabolic states but are difficult to follow locally. Here, we demonstrate a robust and straightforward strategy, transforming the widely used mitochondrial membrane localization fluorophore 10-Nonyl Acridine Orange (NAO) into a multi-functional probe of membrane microenvironments. By monitoring the blinking kinetics of NAO in small unilamellar vesicles, and by computational simulations, we found that NAO exhibits prominent reversible singlet-triplet state transitions and can act as a light-induced Lewis acid forming a red-emissive doublet radical. The resulting blinking kinetics are highly environment sensitive, specifically reflecting local membrane oxygen concentrations, redox conditions, membrane charge, fluidity and lipid compositions, and can also be imaged in live cells, in a spatially resolved manner. They also reflect hydroxyl ion dependent transitions to and from the fluorophore doublet radical, closely coupled to proton transfer events in the membranes, local pH, and two- and three-dimensional buffering properties on and above the membranes. Generally, by the demonstrated blinking imaging strategy existing fluorophore markers can be transformed into multi-parametric microenvironmental sensors. The strategy makes it possible to image local cellular conditions highly relevant to cancer, metabolic and infectious diseases, thereby providing a basis for cellular diagnostics and for fundamental membrane studies.</p>
Mapping of cell types in the tumor microenvironment from tissue images via deep learning trained by spatial transcriptomics of lung adenocarcinoma
<p>Spatial transcriptomic data (10X Visium Platform) of lung adenocarcinoma that comprised thousands of spots with gene expression data and spatially registered H&E-stained tissue images from 22 samples.</p>
LIX1L aggravates NASH-HCC progression by reprogramming of hepatic Metabolism and microenvironment via CD36
GEO Series GSE264479. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
RNA-Seq comparative analysis of human neuroblastoma cells before and after their confrontation to the embryonic microenvironment
GEO Series GSE91377. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Sin3B loss enhances the T-cell inflamed tumor microenvironment through the redistribution of H3K27Ac signals in pancreatic cancer [CUT&Tag]
GEO Series GSE254767. Mus musculus. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Intrahepatic immune microenvironment contributes to spontaneous tolerance in pediatric liver transplantation recipients
GEO Series GSE242205. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
NR4A1 transcriptionally regulates the differentiation of stem-like CD8+ T cells in the tumor microenvironment (RNA-Seq)
GEO Series GSE266287. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
Cancer-associated fibroblast-like tumor cells remodel the Ewing sarcoma tumor microenvironment
GEO Series GSE236289. Homo sapiens. 28 samples. Type: Expression profiling by high throughput sequencing; Other.
A tumor microenvironment-driven network regulated by STAT3 and p65 controls the enrichment of cancer stem cells in human HR+/HER2- breast cancer cells
GEO Series GSE226339. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Gene expression in human (h)T-ALL isolated from NSG mice as a function of the bone marrow microenvironment
GEO Series GSE100718. Homo sapiens. 6 samples. Type: Expression profiling by array.
Acidic microenvironment and transcriptomic genes in pancreatic cancer cells
GEO Series GSE278328. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
NFAT5 induction by the tumor microenvironment enforces CD8 T cell exhaustion (CUT&Tag)
GEO Series GSE237313. Mus musculus. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Sin3B loss enhances the T-cell inflamed tumor microenvironment through the redistribution of H3K27Ac signals in pancreatic cancer [RNA-seq]
GEO Series GSE254770. Mus musculus. 16 samples. Type: Expression profiling by high throughput sequencing.
The metastatic microenvironment. Brain-derived soluble factors alter the malignancy phenotype of cutaneous and brain- metastasizing melanoma cells
GEO Series GSE34970. Homo sapiens. 4 samples. Type: Expression profiling by array.
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.