Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
1,545
datasets available to search
ShareScore release 0.9.0
Dataset results
1,545 results for “microenvironment”
Data from: Linking microenvironment modification to species interactions and demography in an alpine plant community
Open the record for dataset details and reuse information.
Characterization of the tumor-immune microenvironment in hepatocellular carcinoma by highly multiplexed imaging mass cytometry
<p>Imaging mass cytometry data of 54 HCC patients. </p> <ul> <li>DC_img_normalized: Preprocessed and normalized multistack .tiff images. Each stack represents one channel. Channel annotations are stored in the ICICohort_panel.csv file. ROIs are located in the tumor, interface and adjacent liver as indicated in the file name.</li> <li>DC_cellmasks: Masks identifying individual cells on the images.</li> <li>DC_stromamasks: Masks identifying stromal and parenchymal regions on the image.</li> <li>DCCohort_panel.csv: table containing channel information (metal tag and marker).</li> </ul> <p>Patient metadata may be found as supplementary table 2 of DOI <a href="https://doi.org/10.1136/gutjnl-2024-332837" target="_blank" rel="noopener noreferrer"> 10.1136/gutjnl-2024-332837 </a>.</p>
Respiratory Complex I Regulates Dendritic Cell Maturation in Explant Model of Human Tumor Immune Microenvironment
<p>Source data for the paper, "Respiratory Complex I Regulates Dendritic Cell Maturation in Explant Model of Human Tumor Immune Microenvironment."<br><br>This includes nanostring gene expression profiling of primary human tumor material ("fresh" in the data, these samples are taken directly after enzymatic digestion) and the corresponding 3D Patient-Derived Explant Culture (PDEC). <br><br>transfer_257851_files_0a119f4d.zip refers to the mouse spatial transcriptomics data.<br><br>DE_results_Metformin/LPS files refer to differentially expressed genes of human monocyte-derived dendritic cells of 6 individual donors to control untreated dendritic cells after 24hr treatment. <br><br> Also includes the original Seurat.rds file for the scSEQ of primary tumor material (fresh) vs. PDEC<br><br><br><br><br> </p>
A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment
<p>All processed data used in the manuscript 'A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment'. For more detail please refer to the manuscript. If there is any question please contact Bokai Zhu via email: BZHU0@MGH.HARVARD.EDU.</p> <p>Data folder structure:</p> <p>Main data (eg. presented in main figures etc): Please see .zip file 'data_submission.zip'.</p> <p>Additional data (eg. during revision, or other misc files): Please see .zip file 'data_submission_part2.zip'.</p>
QPCTL regulates macrophage and monocyte abundance and inflammatory signatures in the tumor microenvironment
<p><strong>The enzyme glutaminyl-peptide cyclotransferase-like protein (QPCTL) catalyzes the formation of pyroglutamate residues at the NH<sub>2</sub>-terminus of proteins, thereby influencing their biological properties. A number of studies have implicated QPCTL in the regulation of chemokine stability. Furthermore, QPCTL activity has recently been shown to be critical for the formation of the high affinity SIRPa binding site of the CD47 “don’t-eat-me” protein. Based on the latter data, interference with QPCTL activity—and hence CD47 maturation—may be proposed as a means to promote anti-tumor immunity. However, the pleiotropic activity of QPCTL makes it difficult to predict the effects of QPCTL inhibition on the tumor microenvironment (TME). Using a syngeneic mouse melanoma model, we demonstrate that QPCTL deficiency alters the intra-tumoral monocyte-to-macrophage ratio, results in a profound increase in the presence of pro-inflammatory cancer-associated fibroblasts (CAFs) relative to immunosuppressive TGF-b1-driven CAFs, and leads to an increased IFN and decreased TGF-b transcriptional response signature in tumor cells. Importantly, the functional relevance of the observed TME remodeling is demonstrated by the synergy between QPCTL deletion and anti PD-L1 therapy, sensitizing an otherwise refractory melanoma model to anti-checkpoint therapy. Collectively, these data provide support for the development of strategies to interfere with QPCTL activity as a means to promote tumor-specific immunity.</strong></p>
Heterogeneity of RNA editing in mesothelioma and how RNA editing enzyme ADAR2 affects mesothelioma cell growth, response to chemotherapy and tumor microenvironment
<p>Raw data supporting the manuscript</p>
Reconstitution of the multiple myeloma microenvironment following lymphodepletion with BCMA CAR-T therapy
<p>BCMA-targeted CAR-T therapy has shown potent treatment outcomes in treating multiple myeloma (MM), a disease characterized by malignant bone marrow (BM) plasma cells. However, the remodeling of MM microenvironment after CAR-T therapy remains poorly understood. Here, we report the reconstitution of MM microenvironment by obtaining single-cell transcriptomes for paired BM specimens (n = 14) from 7 MM patients before (<em>i.e.</em>, baseline, ''day −4'') and after (<em>i.e.</em>, ''day 28'') post-lymphodepleted BCMA CAR-T therapy. Our analysis revealed heterogeneity in driver gene expression among MM cells, even those harboring the same cytogenetic abnormalities. The best overall responses of patients over the 15-month follow-up are positively correlated with the abundance and targeted cytotoxic activity of CD8<sup>+</sup> effector CAR-T cells on day 28 after CAR-T cell infusion. Additionally, favorable responses are associated with attenuated immunosuppression mediated by regulatory T cells (Tregs), enhanced CD8<sup>+</sup> effector T cell cytotoxic activity, and elevated type 1 conventional dendritic cell (cDC1) antigen presentation ability. DC re-clustering inferred intramedullary-originated cDC3s with extramedullary migration. Cell-cell communication network analysis indicated BCMA CAR-T therapy mitigates BAFF/GALECTIN/MK pathway-mediated immunosuppression and activates MIF pathway-mediated anti-MM immunity. Our study sheds light on MM microenvironment dynamics after BCMA CAR-T therapy, offering clues for predicting treatment responsivity.</p>
Oncogenic calreticulin induces TGF-β expression and Treg expansion in the bone marrow microenvironment as a mechanism of immune escape
<p>This repository contains all necessary scRNA-seq inputs to reproduce the results described in "Oncogenic calreticulin induces TGF-β expression and Treg expansion in the bone marrow microenvironment as a mechanism of immune escape" by Schmidt et al. (Cancer Research 2024). </p> <p>Content:</p> <ol> <li>"MPN_calreticulin_bm.R" --> R script containing all code</li> <li>"cells_table.RDS" --> cells table containing, cell_id, UMAP coordinates, complexity, cell type annotation and metadata</li> <li>"normalized_matrix.RDS" --> quality control filtered, log2-normalized and centered expression matrix</li> <li>"reference_signatures.RDS" --> all external signatures used for this study</li> <li>"EV2_*", "EV5_*", "MPN2_*", "MPN5_*", --> cellranger outputs</li> </ol>
Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment - Nanostring CosMx SMI Data
<p>Data export from Nanostring CosMx SMI, directly from Nanostring, in Seurat Object format for use in R. Clear cell renal cell carcinoma and papillary renal cell carcinoma were profiled before and after exposure to immunotherapy, with and without sarcomatoid features in clear cell tumors. Each tumor had a field of view in the stromal compartment and field of view in the tumor compartment.</p> <p>For appropriate clinical information associated with this study, please contact Dr. Brandon Manley.</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>
Processed CODEX Datasets from - Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens
<p>This entry provides access to processed CODEX data files of three studies analyzed in the article "Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens". Details of datasets can be found in the Methods section of the article.</p> <p>For each dataset:</p> <ul> <li>A comma-separated values (CSV) file containing metadata of regions is included</li> <li>A zip file containing multiple CSV files is included: <ul> <li>`{region_id}.cell_data.csv`, a table containing three columns: "CELL_ID", "X", and "Y". This table provides centroid locations for all cells segmented in this region.</li> <li>`{region_id}.expression.csv`, a table containing multiple columns: "CELL_ID", "DAPI", "CD45", etc. This table provides detailed protein biomarker expression quantified and normalized for all cells in this region.</li> <li>`{region_id}.cell_types.csv`, a table containing two columns: "CELL_ID" and "CELL_TYPE". This table provides cell type annotations for all cells in this region.</li> <li>`{region_id}.cell_features.csv`, a table containing two columns: "CELL_ID" and "SIZE". This table provides morphology descriptors (only containing cell size for these studies) for all cells in this region.</li> </ul> </li> </ul> <p>These data files are also available through the Enable Medicine Public Study page: <a href="https://app.enablemedicine.com/portal/atlas-library/studies/92394a9f-6b48-4897-87de-999614952d94?sid=1168">https://app.enablemedicine.com/portal/atlas-library/studies/92394a9f-6b48-4897-87de-999614952d94?sid=1168</a>. Raw multiplexed immunofluorescence images will be accessible through the visualizer app of Enable Medicine Portal.</p> <p>Codes for this study are stored in <a href="https://gitlab.com/enable-medicine-public/space-gm">https://gitlab.com/enable-medicine-public/space-gm</a>. Please direct all further questions and/or issues to the gitlab repository or lead contact (A.E.T.).</p>
Acidic Microenvironment Enhances Cisplatin Resistance in Bladder Cancer via Bcl-2 and XIAP
Open the record for dataset details and reuse information.
Hepatocellular carcinoma (HCC) Tumor microenvironment is more suppressive than colorectal cancer liver metastasis (CRLM) Tumor microenvironment.
<p><strong>Background and purpose:</strong> While HCC is an inflammation-associated cancer, CRLM develop on permissive healthy liver microenvironment. To evaluate the immune aspects of these two different environments, peripheral blood-(PB), peritumoral-(PT) and tumoral tissues-(TT) from HCC and CRLM patients were evaluated.</p> <p><strong>Methods:</strong> 40 HCC and 34 CRLM were enrolled and freshly TT, PT and PB were collected at the surgery. PB-, PT- and TT-derived CD4<sup>+</sup>CD25<sup>+ </sup>Tregs, M/PMN-MDSC and PB-derived CD4<sup>+</sup>CD25<sup>− </sup>Teffector cells (Teffs) were isolated and characterized. Tregs function was also evaluated in the presence of the CXCR4 inhibitor, Peptide-R29, AMD3100 or anti-PD1. RNA was extracted from PB/PT/TT-tissues and tested for FOXP3, CXCL12, CXCR4, CCL5, IL-15, CXCL5, Arg-1, N-cad, Vim, CXCL8, TGFβ and VEGF-A expression.</p> <p><strong>Results:</strong> In HCC/CRLM-PB higher number of functional Tregs, CD4<sup>+</sup>CD25<sup>hi</sup>FOXP3<sup>+</sup> were detected, although PB-HCC Tregs exert a more suppressive function as compared to CRLM-Tregs. In HCC/CRLM-TT Tregs were highly represented with Activated/ENTPD-1<sup>+</sup>Tregs prevalent in HCC. As compared to CRLM, HCC overexpressed CXCR4 and N-cadherin/Vimentin in a contest rich of arginase and CCL5. Monocytic-MDSCs were highly represented in HCC/CRLM while high Polymorphonuclear-MDSCs were detected only in HCC. Interestingly, CXCR4-PB-Tregs function was impaired in HCC/CRLM by the CXCR4 inhibitor R29.</p> <p><strong>Conclusion:</strong> In HCC and CRLM, peripheral blood, peritumoral and tumoral tissues-Tregs are highly represented and functional. Nevertheless, HCC display a more immunosuppressive TME due to Tregs, MDSCs, intrinsic tumor features (CXCR4, CCL5, arginase) and the contest in which it develops. As CXCR4 is overexpressed in HCC/CRLM tumor/TME cells, CXCR4 inhibitors may be considered for double hits therapy in liver cancer patients.</p>
Deep Learning-based 3D single-cell imaging analysis pipeline for quantifying cell-cell interaction dynamics in the tumor microenvironment
<p>These are 3D live-cell imaging datasets of gastric tumor organoids in co-culture with primary human Natural Killer (NK) cells. The datasets were analyzed by a new, deep learning-based 3D image analysis software tool, SiQ-3D, which we developed and presented in the paper titled "Deep Learning-based 3D single-cell imaging analysis pipeline for quantifying cell-cell interaction dynamics in the tumor microenvironment". Interested users can download the SiQ-3D software code from GitHub (https://github.com/simonlbd1/SiQ-3D) or Code Ocean (https://codeocean.com/capsule/6676007/tree/v2), analyze the 3D image datasets locally, and cross-check the results with the SiQ-3D quantified results that we provided here.</p>
Fragment-sequencing unveils local tissue microenvironments at single-cell resolution
<p>This dataset contains the Resolve dataset that was used in the publication. Other data set can be found in GEO with the accession number GSE216189. The code that was used during the analysis can be found on our GitHub repository: https://github.com/Moors-Code/Fragment-sequencing</p><p> </p><p> </p>
Patient-Derived Tumor Organoid and Fibroblast Assembloid Models for interrogation of the tumor microenvironment in Esophageal Adenocarcinoma
<p>This repository contains original microscopy data from the Sharpe et al. paper, "Patient-Derived Tumor Organoid and Fibroblast Assembloid Models for interrogation of the tumor microenvironment in Esophageal Adenocarcinoma" in Cell Reports Methods 2024.</p> <p>All whole slide images were obtained using an LM dotSlide slide scanning microscope in Olympus .vsi format and can be opened using the BioFormats library (for example, in QuPath). Wholemount immunofluorescent stains were imaged on a Leica SP8 laser-scanning confocal microscope and are presented as .IMS files, which allows for visualization and further analysis of the 3D data in Imaris (Oxford Instruments).</p> <p>Data are arranged in subfolders based on the figure they came from (Figures 1-4).</p>
Reconstitution of the multiple myeloma microenvironment following lymphodepletion with BCMA CAR-T therapy
Open the record for dataset details and reuse information.
Single-cell and spatial RNA sequencing identify divergent microenvironments and progression signatures in early- versus late-onset prostate cancer
Open the record for dataset details and reuse information.
Single-cell multi-modal analysis of tumor microenvironment in human non-small cell lung cancer tissues
Open the record for dataset details and reuse information.
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.