Processed single-cell RNA-seq data for "Evolutionarily conserved transcriptional regulators control monoaminergic neuron development"
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| Sprache: | Englisch |
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2025
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| _version_ | 1866902022294339584 |
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| author | Lewis, Clifton |
| author_facet | Lewis, Clifton |
| contents | <h2><strong>Contents</strong></h2> <table style="border-collapse: collapse; width: 99.9748%;"><colgroup><col style="width: 39.4049%;"><col style="width: 60.5699%;"></colgroup> <tbody> <tr> <td><strong>Folder</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td><strong>1_Replicate_Processed_Objects</strong></td> <td>Processed per-replicate scRNA-seq objects (post-QC, normalized, annotated).</td> </tr> <tr> <td><strong>2_Timepoint_Processed_Objects</strong></td> <td>Integrated, timepoint-specific datasets spanning 0–22 h after egg laying (AEL).</td> </tr> <tr> <td><strong>3_FullDataset_Processed_Objects</strong></td> <td>Full integrated dataset across all developmental stages with annotated cell identities.</td> </tr> <tr> <td><strong>4_MatureNeuronalDataset_Processed_Objects</strong></td> <td>Subset of mature neuronal populations used for trajectory analyses.</td> </tr> <tr> <td><strong>5_MatureNeuronalDataset_Velocity_Objects</strong></td> <td>scVelo-formatted Loom files for RNA velocity analysis.</td> </tr> <tr> <td><strong>6_MatureNeuronalDataset_CellRank_Objects</strong></td> <td>Processed CellRank outputs with fate probabilities and latent-time assignments.</td> </tr> </tbody> </table> <p>---</p> <h2><strong> Usage Notes</strong></h2> <ul> <li>These processed objects can be loaded directly into: <ul> <li>R (Seurat ≥ v5.2)</li> <li>Python (Scanpy / scVelo ≥ v0.3)</li> <li>Refer to the <em>Methods</em> section of the manuscript for detailed data-processing and analysis pipelines.</li> <li>For reproducibility, all analysis scripts are available at: </li> <li> <a href="https://github.com/cliftonlewis/2025_Drosophila_scRNAseq_EmbryoNeurogenesis_Monoamine/">https://github.com/cliftonlewis/2025_Drosophila_scRNAseq_EmbryoNeurogenesis_Monoamine/</a></li> </ul> </li> </ul> <p>---</p> <h2><strong>Keywords</strong></h2> <p>Drosophila • single-cell RNA-seq • embryonic neurogenesis • RNA velocity • CellRank • trajectory analysis • monoaminergic neurons • transcription factors • evolution</p> <p>---</p> <h2><strong>⚖️ License</strong></h2> <p>This repository and dataset are made available under the **MIT License**:</p> <p>Copyright (c) 2025 Clifton Lewis and contributors </p> <p>---</p> <h2><strong>Citation</strong></h2> <p>If you use this dataset, please cite:</p> <p>> Lewis, C., <em>et al.</em> (2025). <em>Evolutionarily conserved transcriptional regulators control monoaminergic neuron development.</em> [Manuscript in preparation / published in *Journal TBD*].</p> <p>---</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_17441737 |
| institution | Zenodo |
| language | eng |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Processed single-cell RNA-seq data for "Evolutionarily conserved transcriptional regulators control monoaminergic neuron development" Lewis, Clifton Drosophila Drosophila/genetics single-cell RNA-seq embryonic neurogenesis RNA velocity CellRank trajectory analysis monoaminergic neurons transcription factors evolution <h2><strong>Contents</strong></h2> <table style="border-collapse: collapse; width: 99.9748%;"><colgroup><col style="width: 39.4049%;"><col style="width: 60.5699%;"></colgroup> <tbody> <tr> <td><strong>Folder</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td><strong>1_Replicate_Processed_Objects</strong></td> <td>Processed per-replicate scRNA-seq objects (post-QC, normalized, annotated).</td> </tr> <tr> <td><strong>2_Timepoint_Processed_Objects</strong></td> <td>Integrated, timepoint-specific datasets spanning 0–22 h after egg laying (AEL).</td> </tr> <tr> <td><strong>3_FullDataset_Processed_Objects</strong></td> <td>Full integrated dataset across all developmental stages with annotated cell identities.</td> </tr> <tr> <td><strong>4_MatureNeuronalDataset_Processed_Objects</strong></td> <td>Subset of mature neuronal populations used for trajectory analyses.</td> </tr> <tr> <td><strong>5_MatureNeuronalDataset_Velocity_Objects</strong></td> <td>scVelo-formatted Loom files for RNA velocity analysis.</td> </tr> <tr> <td><strong>6_MatureNeuronalDataset_CellRank_Objects</strong></td> <td>Processed CellRank outputs with fate probabilities and latent-time assignments.</td> </tr> </tbody> </table> <p>---</p> <h2><strong> Usage Notes</strong></h2> <ul> <li>These processed objects can be loaded directly into: <ul> <li>R (Seurat ≥ v5.2)</li> <li>Python (Scanpy / scVelo ≥ v0.3)</li> <li>Refer to the <em>Methods</em> section of the manuscript for detailed data-processing and analysis pipelines.</li> <li>For reproducibility, all analysis scripts are available at: </li> <li> <a href="https://github.com/cliftonlewis/2025_Drosophila_scRNAseq_EmbryoNeurogenesis_Monoamine/">https://github.com/cliftonlewis/2025_Drosophila_scRNAseq_EmbryoNeurogenesis_Monoamine/</a></li> </ul> </li> </ul> <p>---</p> <h2><strong>Keywords</strong></h2> <p>Drosophila • single-cell RNA-seq • embryonic neurogenesis • RNA velocity • CellRank • trajectory analysis • monoaminergic neurons • transcription factors • evolution</p> <p>---</p> <h2><strong>⚖️ License</strong></h2> <p>This repository and dataset are made available under the **MIT License**:</p> <p>Copyright (c) 2025 Clifton Lewis and contributors </p> <p>---</p> <h2><strong>Citation</strong></h2> <p>If you use this dataset, please cite:</p> <p>> Lewis, C., <em>et al.</em> (2025). <em>Evolutionarily conserved transcriptional regulators control monoaminergic neuron development.</em> [Manuscript in preparation / published in *Journal TBD*].</p> <p>---</p> |
| title | Processed single-cell RNA-seq data for "Evolutionarily conserved transcriptional regulators control monoaminergic neuron development" |
| topic | Drosophila Drosophila/genetics single-cell RNA-seq embryonic neurogenesis RNA velocity CellRank trajectory analysis monoaminergic neurons transcription factors evolution |
| url | https://doi.org/10.5281/zenodo.17441737 |