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308 results for “hiPSCs”
iPlacenta: hIPSC placenta-on-a-chip RNAseq data from 3D vs 2D, day 0 vs day 4 differentiation
<p>RNAseq data from hIPSC dervived trophoblasts seeded in 3D (OrganoPlate) or 2D surface at day 0 or day 4 differentiation. </p> <p>Description of file names found below</p> <table> <tbody> <tr> <td> <p><strong>SampleID/File name</strong></p> </td> <td> <p><strong>Condition- Differentiation day</strong></p> </td> </tr> <tr> <td> <p>iPSC-THB-2D-D0-1</p> </td> <td> <p>2D-Day0</p> </td> </tr> <tr> <td> <p>iPSC-THB-2D-D0-2</p> </td> <td> <p>2D-Day0</p> </td> </tr> <tr> <td> <p>iPSC-THB-2D-D0-3</p> </td> <td> <p>2D-Day0</p> </td> </tr> <tr> <td> <p> </p> </td> <td> <p> </p> </td> </tr> <tr> <td> <p>iPSC-THB-2D-D4-4</p> </td> <td> <p>2D-Day4</p> </td> </tr> <tr> <td> <p>iPSC-THB-2D-D4-5</p> </td> <td> <p>2D-Day4</p> </td> </tr> <tr> <td> <p>iPSC-THB-2D-D4-6</p> </td> <td> <p>2D-Day4</p> </td> </tr> <tr> <td> <p> </p> </td> <td> <p> </p> </td> </tr> <tr> <td> <p>iPSC-THB-3D-D0-7</p> </td> <td> <p>3D-Day0</p> </td> </tr> <tr> <td> <p>iPSC-THB-3D-D0-8</p> </td> <td> <p>3D-Day0</p> </td> </tr> <tr> <td> <p>iPSC-THB-3D-D0-9</p> </td> <td> <p>3D-Day0</p> </td> </tr> <tr> <td> <p> </p> </td> <td> <p> </p> </td> </tr> <tr> <td> <p>iPSC-THB-3D-D4-10</p> </td> <td> <p>3D-Day4</p> </td> </tr> <tr> <td> <p>iPSC-THB-3D-D4-11</p> </td> <td> <p>3D-Day4</p> </td> </tr> <tr> <td> <p>iPSC-THB-3D-D4-12</p> </td> <td> <p>3D-Day4</p> </td> </tr> <tr> <td> <p>iPSC-THB-3D-D4-13</p> </td> <td> <p>3D-Day4</p> </td> </tr> </tbody> </table>
hiPSC 3D immunofluorescence images, test data set 2x2, 10Z
<p>Example dataset of human induced pluripotent stem cells, imaged at 40x magnification with a Yokogawa CV7000. This is a small subset of a larger experiment intended as a test dataset for Fractal: https://github.com/fractal-analytics-platform/fractal</p> <p>3 Channels were imaged:</p> <p>- C01: DAPI, nuclear stain</p> <p>- C02: nanog, antibody staining with Bio-Techne AG, AF1997-SP, Lot KKJ0617121 for the stemness marker nanog</p> <p>- C03: Lamin B1, antibody staining with Abcam, ab16048, Lot GR3244890-2 for the nuclear envelope marker Lamin B1</p> <p> </p> <p>This dataset contains 10 Z levels for 4 field of views for those 3 channels, as well as (manually adjusted) metadata files from the Yokogawa CV7000.</p> <p> </p> <p>The data was acquired in the Pelkmans lab in August 2020. The images have been converted from TIFF into PNG (lossless). </p>
OME-Zarr 3D hiPSCs with 3D labels & 3D measurements, 2x2 field of views
<p>These are 2 small OME-Zarr files of the data from <a href="../records/7057076">10.5281/zenodo.7057076</a>.</p> <p>The images have been processed using <a href="https://fractal-analytics-platform.github.io/">Fractal</a>, the workflow is attached as a json file. It ran with fractal-server==2.3.6, fractal-client==2.0.1, fractal-web==1.4.0 and fractal-tasks-core==1.2.1.</p> <p>Both Zarr files are Zip-compressed to allow easier upload & download from Zenodo. </p> <p>20200812-CardiomyocyteDifferentiation14-Cycle1.zarr contains 3 3D channels, a nuclear segmentation produced by <a href="https://cellpose.readthedocs.io/en/latest/">cellpose</a> as labels and 4 tables: A ROI table for the whole well, a ROI table for the 4 field of views, a masking ROI table for the nuclear segmentation, as well as measurements performed with <a href="https://github.com/haesleinhuepf/napari-skimage-regionprops">napari-skimage-regionprops</a>.</p> <p>20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr contains the same 3 channels, but as maximum intensity projections. It contains nuclear segmentation through cellpose, as well as 3 more labels generated by napari workflows (different thresholds, less accurate segmentations). It also contains 7 tables: The region of interests like in the 3D data, as well as measurements performed with <a href="https://github.com/haesleinhuepf/napari-skimage-regionprops">napari-skimage-regionprops</a>.</p> <p>The tables are stored in the OME-Zarr file according to the <a href="https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/">Fractal table specification</a> spec in AnnData.</p> <p>The 3 channels are:</p> <p>- 0: DAPI, nuclear stain</p> <p>- 1: nanog, antibody staining with Bio-Techne AG, AF1997-SP, Lot KKJ0617121 for the stemness marker nanog</p> <p>- 2: Lamin B1, antibody staining with Abcam, ab16048, Lot GR3244890-2 for the nuclear envelope marker Lamin B1</p>
OME-Zarr hiPSC 3D immunofluorescence images, tiny test set
<p><em>This dataset is intended to be used for automated testing of OME-Zarr processing.</em></p> <p> </p> <p>Example dataset of human induced pluripotent stem cells, imaged at 40x magnification with a Yokogawa CV7000. This is a tiny subset of a larger experiment intended as a test dataset for the <a href="https://fractal-analytics-platform.github.io/">Fractal platform</a> and others experimenting with OME-Zarrs.</p> <p>1 Channel is included:</p> <ul> <li>C01: DAPI, nuclear stain</li> </ul> <p>It is generated from this raw data: <a href="../records/8287221">https://zenodo.org/records/8287221</a></p> <p>This dataset contains 2 Z levels for 2 field of views for this 1 channel, as well as (manually adjusted) metadata files from the Yokogawa CV7000. The data was acquired in the Pelkmans lab in August 2020.</p> <p>The images have been processed using Fractal, the workflow is attached as a json file. It ran with fractal-server==2.3.6, fractal-client==2.0.1, fractal-web==1.4.0 and fractal-tasks-core==1.2.1.</p> <p>Two versions of the OME-Zarr are added here: A 3D version with both Z planes. And a 2D version (MIP of the Z-planes) which also contains label images from cellpose segmentation, measurements and output ROI tables.</p>
hiPSC 3D immunofluorescence images, tiny test set
<p>Example dataset of human induced pluripotent stem cells, imaged at 40x magnification with a Yokogawa CV7000. This is a tiny subset of a larger experiment intended as a test dataset for Fractal: https://github.com/fractal-analytics-platform/fractal</p> <p>It is a subset of this dataset: https://zenodo.org/record/7057076</p> <p>1 Channel is included:</p> <p>- C01: DAPI, nuclear stain</p> <p> </p> <p>This dataset also contains a small Fractal workflow for standard processing</p> <p> </p> <p>This dataset contains 2 Z levels for 2 field of views for this 1 channel, as well as (manually adjusted) metadata files from the Yokogawa CV7000.</p> <p> </p> <p>The data was acquired in the Pelkmans lab in August 2020. The images have been converted from TIFF into PNG (lossless). </p>
OME-Zarr 3D hiPSCs with labels & measurements, 2x2 field of views
<p>These are 2 small OME-Zarr files of the data from <a href="https://doi.org/10.5281/zenodo.7057076">10.5281/zenodo.7057076</a>.</p> <p>They have been processed using <a href="https://pypi.org/project/fractal-client/">fractal-client</a> 0.2.1, <a href="https://pypi.org/project/fractal-server/0.1.2/">fractal-server</a> 0.1.4 and <a href="https://pypi.org/project/fractal-tasks-core/">fractal-tasks-core</a> 0.1.9 using this workflow: <a href="https://github.com/fractal-analytics-platform/fractal/tree/main/examples/08_cardio_2x2_dataset_processing_zenodo">https://github.com/fractal-analytics-platform/fractal/tree/main/examples/08_cardio_2x2_dataset_processing_zenodo</a></p> <p>Both Zarr files are Zip-compressed to allow easier upload & download from Zenodo. </p> <p>20200812-CardiomyocyteDifferentiation14-Cycle1.zarr contains 3 3D channels and a table with regions of interest for the 4 field of views contained in this data.</p> <p>20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr contains the same 3 channels, but as maximum intensity projections. It contains nuclear segmentation through cellpose. It also contains 2 tables: The region of interests like in the 3D data, as well as measurements performed with <a href="https://github.com/haesleinhuepf/napari-skimage-regionprops">napari-skimage-regionprops</a>.</p> <p>The tables are stored in the OME-Zarr file according to the <a href="https://github.com/ome/ngff/pull/64">proposed OME-NGFF</a> table spec in AnnData.</p> <p>The 3 channels are:</p> <p>- 0: DAPI, nuclear stain</p> <p>- 1: nanog, antibody staining with Bio-Techne AG, AF1997-SP, Lot KKJ0617121 for the stemness marker nanog</p> <p>- 2: Lamin B1, antibody staining with Abcam, ab16048, Lot GR3244890-2 for the nuclear envelope marker Lamin B1</p> <p> </p> <p>This updated version now passes the ngff schema validation. A version with 3D segmentation is available here: <a href="https://zenodo.org/record/7144919">https://zenodo.org/record/7144919</a></p>
Data from: In vitro to in vivo extrapolation from three-dimensional hiPSC-derived cardiac microtissues and physiologically based pharmacokinetic modeling to inform next-generation arrythmia risk assessment
<p>Proarrhythmic cardiotoxicity remains a substantial barrier to drug development as well as a major global health challenge. <em>In vitro</em> human pluripotent stem cell-based new approach methodologies have been increasingly proposed and employed as alternatives to existing <em>in vitro</em> and <em>in vivo</em> models that do not accurately recapitulate human cardiac electrophysiology or cardiotoxicity risk. In this study, we expanded the capacity of our previously established three-dimensional human cardiac microtissue model to perform quantitative risk assessment by combining it with a physiologically based pharmacokinetic model, allowing a direct comparison of potentially harmful concentrations predicted <em>in vitro</em> to <em>in vivo</em> therapeutic levels. This approach enabled the measurement of concentration responses and margins of exposure for two physiologically relevant metrics of proarrhythmic risk (<em>i.e.</em>, action potential duration and triangulation assessed by optical mapping) across concentrations spanning three orders of magnitude. The combination of both metrics enabled accurate proarrhythmic risk assessment of four compounds with a range of known proarrhythmic risk profiles (<em>i.e., </em>quinidine, cisapride, ranolazine, and verapamil) and demonstrated close agreement with their known clinical effects. Action potential triangulation was found to be a more sensitive metric for predicting proarrhythmic risk associated with the primary mechanism of concern for pharmaceutical-induced fatal ventricular arrhythmias, delayed cardiac repolarization due to inhibition of the rapid delayed rectifier potassium channel, or hERG channel. This study advances human induced pluripotent stem cell-based three-dimensional cardiac tissue models as new approach methodologies that enable <em>in vitro</em> proarrhythmic risk assessment with high precision of quantitative metrics for understanding clinically relevant cardiotoxicity.</p>
Supplementary videos for the "Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture" manuscript
<p>Supplementary videos for preprint manuscript: </p> <p><em>Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture</em><br> Liuba Dvinskikh, Hugh Sparks, Liliana Brito, Kenneth T MacLeod, Sian E Harding, Christopher Dunsby<br> bioRxiv 2023.01.28.526043; doi: https://doi.org/10.1101/2023.01.28.526043</p> <p>All videos have been rendered with JPEG compression.</p> <p>Shortened video captions (Please see supplementary information document for full caption)<br> <strong>Video 1:</strong> 3D LSFM timelapse of hiPSC-CM undergoing spontaneous calcium transients. <br> <strong>Video 2:</strong> Widefield transillumination timelapse of hiPSC-CM and adult-CM <br> <strong>Video 3:</strong> Widefield fluorescence timelapse of hiPSC-CM and adult CM with synchronized spontaneous calcium transients. <br> <strong>Video 4a:</strong> 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients. <br> <strong>Video 4b</strong>: Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients. <br> <strong>Video 5a:</strong> 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients in a sample without NBleb. <br> <strong>Video 5b</strong>: Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture without NBleb undergoing synchronized spontaneous transients. <br> <strong>Video 6a</strong>: 3D LSFM timelapse of hiPSC-CM and adult-CM co-culture undergoing synchronized spontaneous transients in a sample treated with NBleb. <br> <strong>Video 6b:</strong> Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture with NBleb undergoing synchronized spontaneous transients. <br> <strong>Video 7a:</strong> 3D LSFM timelapse of hiPSC-CM and adult-CM day 0 co-culture undergoing synchronized spontaneous transients in a sample without NBleb. <br> <strong>Video 7b: </strong>Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 0 co-culture without NBleb. </p> <p> </p>
Data from: In vitro to in vivo extrapolation from three-dimensional hiPSC-derived cardiac microtissues and physiologically based pharmacokinetic modeling to inform next-generation arrythmia risk assessment
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Supplementary Files - Transcriptomic analysis of CPM-positive hiPSCs-derived liver progenitor cells in a microfluidic device shows zonation-like patterns.
<p>Supplementary Files for the paper intitled Transcriptomic analysis of CPM-positive hiPSCs-derived liver progenitor cells in a microfluidic device shows zonation-like patterns. </p>
Data for: PIEZO1-HaloTag hiPSCs: bridging molecular, cellular and tissue imaging
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hiPSC-CM and co-culture calcium dynamics videos
<p>Note: This version is now redundant - updated videos are available here: <br> <br> Dvinskikh, Liuba, Sparks, Hugh, Brito, Liliana, MacLeod, Kenneth T, Harding, Sian E, & Dunsby, Chris. (2023, January 29). Supplementary videos for the "Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture" manuscript (Version 1). Zenodo. https://doi.org/10.5281/zenodo.7580163<br> <br> ---------------------------------------------------------------------------------------------</p> <p> </p> <p> </p> <p>Supplementary videos for manuscript " Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocyte in co-culture " <br> The videos included are the following: <br> <br> Video 1: 3D LSFM timelapse of hiPSC-CM undergoing spontaneous calcium transients.<br> Video 2: Widefield transillumination timelapse of hiPSC-CM and adult-CM co-culture.<br> Video 3: Widefield epifluorescence timelapse of hiPSC-CM and adult-CM co-culture<br> Video 4: 3D LSFM timelapse of synchronized transients in hiPSC-CM and adult-CM co-culture.<br> Video 5a: 3D LSFM timelapse of hiPSC-CM and adult-CM co-culture, without NBleb.<br> Video 5b: 3D LSFM timelapse of hiPSC-CM and adult-CM co-culture, with NBleb.<br> </p>
Dataset for Automatic motion estimation with applications to hiPSC-CMs
<p>Supplementary data for paper Automatic motion estimation with applications to hiPSC-CMs</p>
Data from: Simultaneous measurement of excitation-contraction coupling parameters identifies mechanisms underlying contractile responses of hiPSC-derived cardiomyocytes
Cardiomyocytes from human induced pluripotent stem cells (hiPSC-CMs) are increasingly recognized as valuable for determining the effects of drugs on ion channels but they do not always accurately predict contractile responses of the human heart. This is in part attributable to their immaturity but the sensitivity of measurement tools may also be limiting. Measuring action potential, calcium flux or contraction individually misses critical information that is captured when interrogating the complete excitation-contraction coupling cascade simultaneously. Here, we develop an hypothesis-based statistical algorithm that identifies mechanisms of action. We design and build a high-speed optical system to measure action potential, cytosolic calcium and contraction simultaneously using fluorescent sensors. These measurements are automatically processed, quantified and then assessed by the algorithm. Multiplexing these three critical physical features of hiPSC-CMs allows identification of all major drug classes affecting contractility with detection sensitivities higher than individual measurement of action potential, cytosolic calcium or contraction.
Data from: Comparison and optimization of hiPSC forebrain cortical differentiation protocols
Several protocols have been developed for human induced pluripotent stem cell neuronal differentiation. We compare several methods for forebrain cortical neuronal differentiation by assessing cell morphology, immunostaining and gene expression. We evaluate embryoid aggregate vs. monolayer with dual SMAD inhibition differentiation protocols, manual vs. AggreWell aggregate formation, plating substrates, neural progenitor cell (NPC) isolation methods, NPC maintenance and expansion, and astrocyte co-culture. The embryoid aggregate protocol, using a Matrigel substrate, consistently generates a high yield and purity of neurons. NPC isolation by manual selection, enzymatic rosette selection, or FACS all are efficient, but exhibit some differences in resulting cell populations. Expansion of NPCs as neural aggregates yields higher cell purity than expansion in a monolayer. Finally, co-culture of iPSC-derived neurons with astrocytes increases neuronal maturity by day 40. This study directly compares commonly employed methods for neuronal differentiation of iPSCs, and can be used as a resource for choosing between various differentiation protocols.
Data from: Simultaneous measurement of excitation-contraction coupling parameters identifies mechanisms underlying contractile responses of hiPSC-derived cardiomyocytes
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Data from: Comparison and optimization of hiPSC forebrain cortical differentiation protocols
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Analysis of single cell gene expression profile in hiPSC-derived NPCs
GEO Series GSE151642. Homo sapiens. 96 samples. Type: Expression profiling by high throughput sequencing; Other.
Bulk RNA-seq of neuromuscular system models generated from human induced pluripotent stem cells (hiPSCs)
GEO Series GSE226477. Homo sapiens. 15 samples. Type: Expression profiling by high throughput sequencing.
Single cell transcriptomics of hiPSC-derived forward programmed megakaryocytes
GEO Series GSE121579. Homo sapiens. 192 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.