| dc.contributor.author |
Silva, Mariana Rodrigues da |
|
| dc.contributor.author |
Jesus, Marcelo Bispo de |
|
| dc.date |
2025-02-21 |
|
| dc.date.accessioned |
2025-01-21 |
|
| dc.date.accessioned |
2025-02-23T01:11:25Z |
|
| dc.date.available |
2025-02-23T01:11:25Z |
|
| dc.identifier.uri |
https://doi.org/10.25824/redu/2BRSM6 |
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| dc.identifier.uri |
https://redu.unicamp.br/dataset.xhtml?persistentId=doi:10.25824/redu/2BRSM6 |
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| dc.description |
<h1>Hepatotoxicity Assessment of Microplastics in Huh7 and HepG2 Cells through High-Content Analysis</h1>
<p>This repository contains the following resources produced during the Master’s research of <strong>Mariana Rodrigues da Silva</strong> at the <em>NanoCell Interactions Lab</em>, University of Campinas (UNICAMP), which focused on investigating the <strong>in vitro hepatotoxicity</strong> of microplastics (PS-MPs) using <strong>HepG2</strong> and <strong>Huh7</strong> cell lines, image-based assays (<strong>High-Content Analysis</strong>), and cellular profiling.</p>
<p>The four main folders are organized as follows:</p>
<pre>
├── Cellpose_Models
│ ├── Calcein-PI-Hoechst
│ ├── Total-Association-of-PS-MPs
│ ├── CellPainting
│ └── LiveCellPainting
├── CellProfiler_Pipelines
│ ├── Calcein-PI-Hoechst
│ ├── Total-Association-of-PS-MPs
│ ├── LiveCellPainting
│ └── CellPainting
├── Images
│ ├── Calcein-PI-Hoechst
│ ├── Total-Association-of-PS-MPs
│ ├── LiveCellPainting
│ └── CellPainting
└── Jupyter_Notebooks
</pre>
<h2>Description of Each Folder:</h2>
<h3><strong>Cellpose_Models</strong>:</h3>
<p>Contains trained models using <strong>Cellpose (version 2.2.3)</strong> for segmenting cellular structures (cells and/or nuclei) in Huh7 and HepG2 cell lines. Each subfolder corresponds to a specific imaging assay.</p>
<h3><strong>CellProfiler_Pipelines</strong>:</h3>
<p>Contains pipelines developed in <strong>CellProfiler (version 4.2.5)</strong> to extract cellular features from Huh7 and HepG2 cell lines. Each subfolder corresponds to a specific imaging assay.</p>
<h3><strong>Images</strong>:</h3>
<p>Contains raw image datasets for each imaging assay, organized into subfolders by assay name. Each subfolder contains two subfolders corresponding to the cell type (<strong>Huh7</strong> or <strong>HepG2</strong>; except for <code>CellPainting</code>, which only contains Huh7). These folders are further subdivided into three independent replicate folders, each containing a subfolder named <code>platemap</code> with the plate layout for the 96-well plate used during image acquisition. The metadata specifies the compounds and concentrations used to treat each well.</p>
<p>The cells were stained using six imaging panels:</p>
<ol>
<li><strong>Calcein-PI-Hoechst</strong> (cell viability assay):
<ul>
<li>Images acquired with a <strong>10× objective</strong> on the Cytation 5 using the following LED cube channels:</li>
<li><strong>DAPI</strong>: nuclei of total cells (excitation/emission = 377/447 nm)</li>
<li><strong>GFP</strong>: live cells (excitation/emission = 445/510 nm)</li>
<li><strong>PI</strong>: dead cells (excitation/emission = 531/647 nm)</li>
</ul>
</li>
<li><strong>Total Association of PS-MPs with Cells Over Time</strong> (interaction assay between cells and fluorescent PS-MPs over time):
<ul>
<li>Images acquired with a <strong>20× objective</strong> on the Cytation 5 using the following LED cube channels:</li>
<li><strong>DAPI</strong>: nuclei (excitation/emission = 377/447 nm)</li>
<li><strong>GFP</strong>: live cells (excitation/emission = 445/510 nm)</li>
<li><strong>PI</strong>: PS-MPs (excitation/emission = 531/647 nm)</li>
</ul>
</li>
<li><strong>Live Cell Painting</strong> (cell profiling assay, Garcia-Fossa et al., 2024; <a href="https://doi.org/10.1101/2024.08.28.610144">DOI</a>):
<ul>
<li>Images acquired with a <strong>20× objective</strong> on the Cytation 5 using the following LED cube channels:</li>
<li><strong>DAPI</strong>: nuclei (excitation/emission = 377/447 nm)</li>
<li><strong>GFP</strong>: nuclei, nucleoli, cytoplasm (excitation/emission = 445/510 nm)</li>
<li><strong>PI</strong>: acidic vesicles (excitation/emission = 531/647 nm)</li>
</ul>
</li>
<li><strong>Cell Painting</strong> (cell profiling assay, Bray et al., 2016; <a href="https://doi.org/10.1038/nprot.2016.105">DOI</a>):
<ul>
<li>Images acquired with a <strong>20× objective</strong> on the Cytation 5 using the following LED cube channels:</li>
<li><strong>DAPI</strong>: plasma membrane and nuclei (excitation/emission = 377/447 nm)</li>
<li><strong>GFP</strong>: endoplasmic reticulum (excitation/emission = 445/510 nm)</li>
<li><strong>PI</strong>: actin cytoskeleton and Golgi complex (excitation/emission = 531/647 nm)</li>
<li><strong>CY5</strong>: mitochondria (excitation/emission = 628/685 nm)</li>
</ul>
</li>
</ol>
<h3><strong>Jupyter_Notebooks</strong>:</h3>
<p>This folder contains:</p>
<ul>
<li><strong>Data processing templates</strong> for normalization, aggregation, annotation, and feature selection.</li>
<li>Templates for identifying cellular profiles using <strong>Linear Discriminant Analysis (LDA)</strong>.</li>
<li><strong>Clustering methods</strong>, including Elbow Method, Silhouette Method, and K-means.</li>
<li><strong>Confusion matrix analysis</strong> to evaluate clustering quality.</li>
<li><strong>Feature importance identification</strong> scripts.</li>
<li>Templates for <strong>statistical analysis</strong>, including Kruskal-Wallis tests with Bonferroni post hoc correction and boxplot visualization of individual features.</li>
</ul>
<hr>
<p>These resources were developed to facilitate <strong>image-based workflows</strong> and advanced data analysis for understanding the hepatotoxic effects of microplastics in vitro.</p> |
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| dc.description.sponsorship |
Fundação de Amparo à Pesquisa do Estado de São Paulo |
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| dc.description.sponsorship |
Fundação de Amparo à Pesquisa do Estado de São Paulo |
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| dc.format |
application/x-gzip |
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| dc.format |
application/x-gzip |
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| dc.format |
application/x-gzip |
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| dc.format |
application/x-gzip |
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| dc.format |
application/x-gzip |
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| dc.format |
application/x-gzip |
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| dc.format |
application/x-gzip |
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| dc.publisher |
Bispo de Jesus, Marcelo |
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| dc.subject |
Medicine, Health and Life Sciences |
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| dc.title |
Hepatotoxicity assessment of microplastics in Huh7 and HepG2 cells through high-content analysis |
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| dc.description.sponsorshipId |
FAPESP: 2022/07854-4 |
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| dc.description.sponsorshipId |
FAPESP: 23/06143-0 |
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