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31 results for “Cellular microenvironment”
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>
Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease
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Spatiotemporal Profiling Unveiling the Cellular Organization Patterns and Local Protumoral Immune Microenvironment Remodeling in Early Lung Adenocarcinoma Progression
<p>Spatial cellular organization patterns (COPs) in tumor microenvironment influence the tumor progression and therapeutic response, however, little is known about the cellular composition and functional potential of these multicellular structures during lung adenocarcinoma progression. Here, we integrate spatial transcriptomics with single cell RNA sequencing to characterize the local tumor and immunological landscape of samples from 8 patients with lung adenocarcinoma at different pathological stages. We identified ten COPs that show distinct associations with local immune states and clinical outcomes, including survival and therapy response. The local infiltration levels of regulatory and dysfunctional immune cells are increased with pathological progression. Cell-to-cell interactions between malignant cells and tumor microenvironment (TME) cells were involved in protumor immune state remodeling. Finally, we detected a group of malignant cells that were specifically located at the tumor boundary, representing a more aggressive state, were involved in the invasion of invasive adenocarcinoma (IAC). Altogether, these results can improve our understanding of the local microenvironment characteristics that underlie LUAD progression and may facilitate the identification of drug targets to prevent invasive progression and biomarkers for diagnosis.</p><p>If you're going to use this dataset, please cite 'Haojie Chen et al. 2023. Protumoral Immune Microenvironment Remodeling in Early Lung Adenocarcinoma Progression. bioRxiv. https://doi.org/10.1101/2023.10.29.564580'</p>
Processed CODEX multiplexed imaging data of cellular microenvironment around T cell stimulating hydrogels
<p>Our research used CODEX (Co-Detection by Indexing) multiplexed imaging to gain insights into the cellular microenvironment surrounding T cell stimulating hydrogels. These hydrogels were engineered with signals that could locally expand antigen-specific T cells for use in tumor immunotherapy. CODEX imaging involves an iterative process of annealing and stripping fluorophore-labeled oligonucleotide barcodes, complementing the barcodes attached to over 40 antibodies used for tissue staining. Subsequently, images underwent standard CODEX image processing (tile stitching, drift compensation, cycle concatenation, background subtraction, deconvolution, and determination of best focal plane), single cell segmentation, and column marker z-normalization by tissue.</p> <p>Our datasets comprise individual cells as rows, each characterized by 40+ antibody fluorescence values quantified from various markers evaluated for each study. These markers correspond to the antibodies targeting specific proteins within the tissue, quantified at the single-cell level. The values represent per-cell/area-averaged fluorescent intensities, z-normalized along each column. Each cell is mapped with its cell type, defined by x and y coordinates representing pixel locations in the original image. </p> <p>We then used this data to investigate how different proportions of the cell types change over time in response to the stimulating hydrogel injection with antigen-specific T cells. These data could be used to understand the cellular interactions, composition, and structure of T cell stimulating biomaterials for antigen-specific immunotherapy and with adoptive T cell transfer. These datasets offer valuable insights for researchers interested in engineering T cell stimulating microenvironments, immune responses, and therapeutic interventions such as T cell therapies.</p> <p>We investigate the dynamic interplay between immune responses, antigen-specific T cell interactions, and hydrogel environment in a murine melanoma model. We injected antigen-specific T cells with microparticle T cell stimulating hydrogels into mice subcutaneously. Injection sites were take out at different time points day=0 (just after injection), day=3, and day=9 (n=3-6 per time point). Our 51-plex CODEX antibody panel characterizes immune cell types, T cell phenotypes, and stromal cell types, resulting in a rich dataset of 241,685 cells across 51 marker channels.</p>
Targeting Microenvironment and Cellular Immunity in Sarcomas Weekly Trabectedin Combined With Metronomic Cyclophosphamide
ClinicalTrials.gov study NCT02805725. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Processed CODEX multiplexed imaging data of cellular microenvironment around T cell stimulating hydrogels
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Analysis of cellular heterogeneity in immune microenvironment of Primary central nervous system lymphoma by single cell sequencing
GEO Series GSE181304. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
Impact of the physical cellular microenvironment on the structure and function of a hepatocytes for drug toxicity applications
GEO Series GSE236919. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Three-dimensional bioprinting enables creation of tissue-informed glioblastoma microenvironments for modeling complex cellular interactions
GEO Series GSE147147. Homo sapiens. 15 samples. Type: Expression profiling by high throughput sequencing.
Single-cell transcriptomic profiling uncovers cellular complexity and microenvironment in gastric tumorigenesis associated with Helicobacter pylori
GEO Series GSE249874. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
Single-cell RNA sequencing reveals different cellular states in malignant cells and the tumor microenvironment in primary and metastatic ER-positive breast cancer
GEO Series GSE306201. Homo sapiens. 22 samples. Type: Expression profiling by high throughput sequencing; Other.
Single-cell landscape of the cellular microenvironment in three different colonic polyp subtypes in children
GEO Series GSE244542. Homo sapiens. 20 samples. Type: Expression profiling by high throughput sequencing.
Coordinated immune networks in leukemia bone marrow microenvironments distinguish response to cellular therapy
GEO Series GSE255530. Homo sapiens. 132 samples. Type: Expression profiling by high throughput sequencing; Other.
The single-cell Atlas of Cellular Heterogeneity and The Immunosuppressive Microenvironment of Brain Metastasis from laryngeal squamous cell carcinoma
GEO Series GSE248388. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
The Effects of Aging on the Molecular and Cellular Composition of the Prostate Microenvironment
GEO Series GSE21542. Mus musculus. 40 samples. Type: Expression profiling by array.
Mechanisms of cellular crosstalk in the gastric tumour microenvironment are mediated by YAP1 and STAT3
GEO Series GSE197002. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Cellular responses in the airway ciliary microenvironment from mouse models of primary ciliary dyskinesia with central pair apparatus defects
GEO Series GSE254100. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Extracellular vesicle-mediated RNA transfer contributes to inter-cellular communication in the liver tumor microenvironment
GEO Series GSE196131. Homo sapiens. 8 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Identifying a high-risk cellular signature in the multiple myeloma bone marrow microenvironment_3
GEO Series GSE136398. Homo sapiens. 131 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)
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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.