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.
278
datasets available to search
ShareScore release 0.9.0
Dataset results
278 results for “cytometry”
HOT Primary Production and Flow Cytometry v2022
<p>This dataset consists of measurements of photosynthetic primary production, chlorophyll a and phaeopigment concentrations, and flow cytometry-based determinations of the abundances of heterotrophic bacteria and the picophytoplankton - Prochlorococcus, Synechococcus and small eukaryotic phytoplankton. All samples were collected through the Hawaii Ocean Time-series (HOT) program, which began in 1988 with ~monthly cruises to Station ALOHA (A Long-term Oligotrophic Habitat Assessment; 22° 10 N, 158° 00 W). Photosynthetic production of organic matter was measured by the 14C tracer method. Details on the methods employed over the years are detailed in Karl et al., Progress in Oceanography (https://doi.org/10.1016/j.pocean.2021.102563). Flow cytometry-based determinations of microbial abundances were made using an EPICS 753 flow cytometer on HOT 22-173 (December 1980 – September 2005) and a B/D Influx flow cytometer beginning with HOT 174 . Details on the flow cytometry methods are provided at (https://hahana.soest.hawaii.edu/hot/methods/bact.html). Samples for chlorophyll a and phaeopigments were collected onto Whatman GF/F filters and extracted with 100% acetone and measured on a Turner Designs Model 10-AU fluorometer based on standard techniques described in Strickland and Parsons, 1972. Method details available at (https://hahana.soest.hawaii.edu/hot/methods/chl.html). Time is in a separate column from date. Dates and times are in local time (HST).</p>
RUCova: Removal of Unwanted Covariance in mass cytometry data
<p>Mass cytometry data, cell area measurement data, and R Markdown reports to reproduce the figures of our publication and understand the application of RUCova.</p> <p>Raw data were saved post de-convolution and spillover-compensation. Gates for singlets and non-dead cells (low_Pt) are included as logical columns and should be applied prior to usage.</p> <p>Mass cytometry data sets:</p> <ul> <li>data1_HNSCC.csv -> Data from 10 Head-and-neck squamous cell carcinoma (HNSCC) cell lines in control condition and 48 h after irradiation with 10 Gy. <ul> <li>marker_category_HNSCC.csv -> table for each marker in the mass cytometry panel and category.</li> </ul> </li> <li>data2_FACS.csv -> Data from Cal33 cell line under different stimuli and FACS-sorted by size (small and large). <ul> <li>size_gates.png -> Image depicting the FACS sorting.</li> </ul> </li> <li>data3_ru.csv -> Data from Cal33 cell line with Ruthenium staining (Rapsomaniki et. al. 2018, doi: <span>10.1038/s41467-018-03005-5</span><span>).</span></li> <li>data_ruthenium_rapsomaniki.csv (data from Rapsomaniki et. al. 2018) </li> </ul> <p>Cell area measurement data:</p> <ul> <li>cell_area_HNSCC.csv -> Measurements of the cell area [µm^2] via microscopy images for the 10 HNSCC in control condition and after irradiation with 10 Gy.</li> </ul> <p>R Markdown reports:</p> <ul> <li>analysis.Rmd </li> <li>analysis.html</li> </ul>
Microscopy and flow cytometry raw data for: A genetically encoded biosensor to monitor dynamic changes of c-di-GMP with high temporal resolution
<p><br>This repository contains the microscopy and flow cytometry raw data for the following publication:</p> <p><strong>A genetically encoded biosensor to monitor dynamic changes of c-di-GMP with high temporal resolution</strong></p> <p>Andreas Kaczmarczyk, Simon van Vliet, Roman Peter Jakob, Raphael Dias Teixeira, Inga Scheidat, Alberto Reinders, Alexander Klotz, Timm Maier, Urs Jenal</p> <p>Biozentrum, University of Basel, 4056 Basel, Switzerland</p> <p>Correspondence to: urs.jenal[at]unibas.ch, andreas.kaczmarczyk[at]unibas.ch</p>
Flow cytometry changes in murine XBP1 KO fed high fat diet
<p>Nonalcoholic fatty liver disease (NAFLD) is one of the most common causes of liver diseases in the United States and can progress to cirrhosis, end-stage liver disease and need for liver transplantation. There are limited therapies for NAFLD, in part, due to incomplete understanding of the disease pathogenesis, which involves different cell populations in the liver. Endoplasmic reticulum stress and its adaptative unfolded protein response (UPR) signaling pathway have been implicated in the progression from simple hepatic steatosis to nonalcoholic steatohepatitis (NASH). We have previously shown that mice lacking the UPR protein X-box binding protein 1 (XBP1) in the liver demonstrated enhanced liver injury and fibrosis in a high fat sugar (HFS) dietary model of NAFLD. In this study, to better understand the role of liver XBP1 in the pathobiology of NAFLD, we fed hepatocyte XBP1 deficient mice a HFS diet or chow and investigated UPR and other cell signaling pathways in hepatocytes, hepatic stellate cells and immune cells. We demonstrate that loss of XBP1 in hepatocytes increased inflammatory pathway expression and altered expression of the UPR signaling in hepatocytes and was associated with enhanced hepatic stellate cell activation after HFS feeding. We believe that a better understanding of liver cell-specific signaling in the pathogenesis of NASH may allow us to identify new therapeutic targets.</p>
Flow cytometry data of intestinal immune cells related to Seumetry toolkit for analysis of high-dimensional flow and mass cytometry data
Open the record for dataset details and reuse information.
Mass cytometry data of immune cells in mice that had experienced explosions.
<p>Mass cytometry was used to assess the expression of immune markers and intracellular proteins in immune cells collected from mice that had experienced explosions. Following mass cytometry detection, .fcs files were generated. The raw data were packaged and uploaded.</p>
Flow cytometry data of "MINCLE and TLR9 agonists synergize to induce sustained Th1/Th17 vaccine memory and potent mucosal recall in Mice and Non-Human Primates"
Open the record for dataset details and reuse information.
CTC identification and characterization in lung cancer using K/V protocol and imaging flow cytometry - part 2
<p>This project is a part of bigger study aiming to identify and characterize circulating tumor cells (CTCs) in peripheral blood of cancer patients. Here, specificaly it focused on CTCs analysis in 29 lung cancer patients. Fraction of peripheral blood mononuclear cells putatively containing CTCs was isolated using density gradient centrifugation. Pan-keratin/vimentin/CD45/CD31/DAPI immunofluorescent staining was performer and DAPI+ or DAPI+CD45/CD31- objects were collected using Amnis® ImageStream®XMk II, Cytek® Biosciences, Inc (lasers: 405 nm, 488 nm, 642 nm, magnification 40x, slow speed flow).</p>
CTC identification and characterization in breast cancer using K/V protocol and imaging flow cytometry - part 1
<p>This project is a part of bigger study aiming to identify and characterize circulating tumor cells (CTCs) in peripheral blood of cancer patients. Here, specificaly it focused on CTCs analysis in 54 breast cancer patients. Fraction of peripheral blood mononuclear cells putatively containing CTCs was isolated using density gradient centrifugation. Pan-keratin/vimentin/CD45/CD31/DAPI immunofluorescent staining was performer and DAPI+ or DAPI+CD45/CD31- objects were collected using Amnis® ImageStream®XMk II, Cytek® Biosciences, Inc (lasers: 405 nm, 488 nm, 642 nm, magnification 40x, slow speed flow).</p>
CTC identification and characterization in lung cancer using K/V protocol and imaging flow cytometry - part 1
<p>This project is a part of bigger study aiming to identify and characterize circulating tumor cells (CTCs) in peripheral blood of cancer patients. Here, specificaly it focused on CTCs analysis in 29 lung cancer patients. Fraction of peripheral blood mononuclear cells putatively containing CTCs was isolated using density gradient centrifugation. Pan-keratin/vimentin/CD45/CD31/DAPI immunofluorescent staining was performer and DAPI+ or DAPI+CD45/CD31- objects were collected using Amnis® ImageStream®XMk II, Cytek® Biosciences, Inc (lasers: 405 nm, 488 nm, 642 nm, magnification 40x, slow speed flow).</p>
CTC identification and characterization in breast cancer using K/V protocol and imaging flow cytometry - part 2
<p>This project is a part of bigger study aiming to identify and characterize circulating tumor cells (CTCs) in peripheral blood of cancer patients. Here, specificaly it focused on CTCs analysis in 54 breast cancer patients. Fraction of peripheral blood mononuclear cells putatively containing CTCs was isolated using density gradient centrifugation. Pan-keratin/vimentin/CD45/CD31/DAPI immunofluorescent staining was performer and DAPI+ or DAPI+CD45/CD31- objects were collected using Amnis® ImageStream®XMk II, Cytek® Biosciences, Inc (lasers: 405 nm, 488 nm, 642 nm, magnification 40x, slow speed flow).</p>
CTC identification and characterization in breast cancer using K/V protocol and imaging flow cytometry - part 4
<p>This project is a part of bigger study aiming to identify and characterize circulating tumor cells (CTCs) in peripheral blood of cancer patients. Here, specificaly it focused on CTCs analysis in 54 breast cancer patients. Fraction of peripheral blood mononuclear cells putatively containing CTCs was isolated using density gradient centrifugation. Pan-keratin/vimentin/CD45/CD31/DAPI immunofluorescent staining was performer and DAPI+ or DAPI+CD45/CD31- objects were collected using Amnis® ImageStream®XMk II, Cytek® Biosciences, Inc (lasers: 405 nm, 488 nm, 642 nm, magnification 40x, slow speed flow).</p>
CTC identification and characterization in breast cancer using K/V protocol and imaging flow cytometry - part 3
<div> <p>This project is a part of bigger study aiming to identify and characterize circulating tumor cells (CTCs) in peripheral blood of cancer patients. Here, specificaly it focused on CTCs analysis in 54 breast cancer patients. Fraction of peripheral blood mononuclear cells putatively containing CTCs was isolated using density gradient centrifugation. Pan-keratin/vimentin/CD45/CD31/DAPI immunofluorescent staining was performer and DAPI+ or DAPI+CD45/CD31- objects were collected using Amnis® ImageStream®XMk II, Cytek® Biosciences, Inc (lasers: 405 nm, 488 nm, 642 nm, magnification 40x, slow speed flow).</p> </div>
CTC identification and characterization in ovarian cancer using K/V protocol and imaging flow cytometry
<p>This project is a part of bigger study aiming to identify and characterize circulating tumor cells (CTCs) in peripheral blood of cancer patients. Here, specificaly it focused on CTCs analysis in 24 ovarian cancer patients. Fraction of peripheral blood mononuclear cells putatively containing CTCs was isolated using density gradient centrifugation. Pan-keratin/vimentin/CD45/CD31/DAPI immunofluorescent staining was performer and DAPI+ or DAPI+CD45/CD31- objects were collected using Amnis® ImageStream®XMk II, Cytek® Biosciences, Inc (lasers: 405 nm, 488 nm, 642 nm, magnification 40x, slow speed flow).</p>
CTC identification and characterization in lung cancer using K/V protocol and imaging flow cytometry - part 2
<p>This project is a part of bigger study aiming to identify and characterize circulating tumor cells (CTCs) in peripheral blood of cancer patients. Here, specificaly it focused on CTCs analysis in 29 lung cancer patients. Fraction of peripheral blood mononuclear cells putatively containing CTCs was isolated using density gradient centrifugation. Pan-keratin/vimentin/CD45/CD31/DAPI immunofluorescent staining was performer and DAPI+ or DAPI+CD45/CD31- objects were collected using Amnis® ImageStream®XMk II, Cytek® Biosciences, Inc (lasers: 405 nm, 488 nm, 642 nm, magnification 40x, slow speed flow).</p>
CTC identification and characterization in prostate cancer using K/V protocol and imaging flow cytometry - part 1
<p>This project aimed to identify and characterize circulating tumor cells (CTCs) in peripheral blood of 33 prostate cancer patients. Fraction of peripheral blood mononuclear cells putatively containing CTCs was isolated using density gradient centrifugation. Pan-keratin/vimentin/CD45/CD31/DAPI immunofluorescent staining was performer and DAPI+ or DAPI+CD45/CD31- objects were collected using Amnis® ImageStream®XMk II, Cytek® Biosciences, Inc (lasers: 405 nm, 488 nm, 642 nm, magnification 40x, slow speed flow).</p>
CTC identification and characterization in prostate cancer using K/V protocol and imaging flow cytometry - part 3
<p>This project aimed to identify and characterize circulating tumor cells (CTCs) in peripheral blood of 33 prostate cancer patients. Fraction of peripheral blood mononuclear cells putatively containing CTCs was isolated using density gradient centrifugation. Pan-keratin/vimentin/CD45/CD31/DAPI immunofluorescent staining was performer and DAPI+ or DAPI+CD45/CD31- objects were collected using Amnis® ImageStream®XMk II, Cytek® Biosciences, Inc (lasers: 405 nm, 488 nm, 642 nm, magnification 40x, slow speed flow).</p>
CTC identification and characterization in prostate cancer using K/V protocol and imaging flow cytometry - part 12
<p>This project aimed to identify and characterize circulating tumor cells (CTCs) in peripheral blood of 33 prostate cancer patients. Fraction of peripheral blood mononuclear cells putatively containing CTCs was isolated using density gradient centrifugation. Pan-keratin/vimentin/CD45/CD31/DAPI immunofluorescent staining was performer and DAPI+ or DAPI+CD45/CD31- objects were collected using Amnis® ImageStream®XMk II, Cytek® Biosciences, Inc (lasers: 405 nm, 488 nm, 642 nm, magnification 40x, slow speed flow).</p>
CTC identification and characterization in prostate cancer using K/V protocol and imaging flow cytometry - part 8
<p>This project aimed to identify and characterize circulating tumor cells (CTCs) in peripheral blood of 33 prostate cancer patients. Fraction of peripheral blood mononuclear cells putatively containing CTCs was isolated using density gradient centrifugation. Pan-keratin/vimentin/CD45/CD31/DAPI immunofluorescent staining was performer and DAPI+ or DAPI+CD45/CD31- objects were collected using Amnis® ImageStream®XMk II, Cytek® Biosciences, Inc (lasers: 405 nm, 488 nm, 642 nm, magnification 40x, slow speed flow).</p>
CTC identification and characterization in prostate cancer using K/V protocol and imaging flow cytometry - part 5
<p>This project aimed to identify and characterize circulating tumor cells (CTCs) in peripheral blood of 33 prostate cancer patients. Fraction of peripheral blood mononuclear cells putatively containing CTCs was isolated using density gradient centrifugation. Pan-keratin/vimentin/CD45/CD31/DAPI immunofluorescent staining was performer and DAPI+ or DAPI+CD45/CD31- objects were collected using Amnis® ImageStream®XMk II, Cytek® Biosciences, Inc (lasers: 405 nm, 488 nm, 642 nm, magnification 40x, slow speed flow).</p>
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.