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| Status |
Public on Apr 18, 2023 |
| Title |
SCENIC+: identification of enhancers and gene regulatory networks using single-cell multiomics (Cortex) |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Joint profiling of chromatin accessibility and gene expression of individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (eGRN). Here we present a new method for the inference of eGRNs, called SCENIC+. SCENIC+ predicts genomic enhancers along with candidate upstream transcription factors (TF) and links these enhancers to candidate target genes. Specific TFs for each cell type or cell state are predicted based on the concordance of TF binding site accessibility, TF expression, and target gene expression. To improve both recall and precision of TF identification, we curated and clustered more than 40,000 position weight matrices that we could associate with ~1,500 human TFs. We validated and benchmarked each of the SCENIC+ components on diverse data sets from different species, including human peripheral blood mononuclear cell types, human ENCODE cell lines, human melanoma cell states, and Drosophila retinal development. Next, we exploit SCENIC+ predictions to study conserved TFs, enhancers, and GRNs between human and mouse cell types in the cerebral cortex. Finally, we provide new capabilities that exploit the inferred eGRNs to study the dynamics of gene regulation along differentiation trajectories; to map regulatory activities onto tissues using spatial omics data; and to predict the effect of TF perturbations on cell state. SCENIC+ provides critical insight into gene regulation, starting from multi-ome atlases of scATAC-seq and scRNA-seq. The SCENIC+ suite is available as a set of Python modules at scenicplus.readthedocs.io.
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| Overall design |
10x single cell multiome on the mouse cortex
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| Contributor(s) |
González-Blas CB, De Winter S, Aerts S |
| Citation(s) |
37443338 |
| |
| Submission date |
Aug 08, 2022 |
| Last update date |
Jul 18, 2023 |
| Contact name |
Gert Hulselmans |
| E-mail(s) |
[email protected]
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| Organization name |
VIB
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| Department |
Center for Brain and Disease Research
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| Lab |
Laboratory of Computational Biology
|
| Street address |
Herestraat 49 PO Box 602
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| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (10)
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| GSM6436470 |
10x multiome (ATAC) on the mouse cortex using the '10x complex UC' protocol |
| GSM6436471 |
10x multiome (RNA) on the mouse cortex using the '10x complex UC' protocol |
| GSM6436472 |
10x multiome (ATAC) on the mouse cortex using the '10x complex' protocol |
| GSM6436473 |
10x multiome (RNA) on the mouse cortex using the '10x complex' protocol |
| GSM6436474 |
10x multiome (ATAC) on the mouse cortex using the 'no permiabilization' protocol |
| GSM6436475 |
10x multiome (RNA) on the mouse cortex using the 'no permiabilization' protocol |
| GSM6436476 |
10x multiome (ATAC) on the mouse cortex using the 'TST_NP40_004' protocol |
| GSM6436477 |
10x multiome (RNA) on the mouse cortex using the 'TST_NP40_004' protocol |
| GSM6436478 |
10x multiome (ATAC) on the mouse cortex using the 'TST' protocol |
| GSM6436479 |
10x multiome (RNA) on the mouse cortex using the 'TST' protocol |
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| This SubSeries is part of SuperSeries: |
| GSE210749 |
SCENIC+: identification of enhancers and gene regulatory networks using single-cell multiomics |
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| Relations |
| BioProject |
PRJNA867356 |
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