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| Status |
Public on Jun 16, 2022 |
| Title |
Shared enhancer gene regulatory networks between wound and oncogenic programs [Multiome] |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Wound response programs are often activated during neoplastic growth in tumors. In both systems, cells respond to acute stress and balance the activation of multiple programs including apoptosis, proliferation, and cell migration. Central to this response are the JNK/MAPK and JAK/STAT signaling pathways. Yet, to what extent these signaling cascades interact at the cis-regulatory level, and how they orchestrate different phenotypic responses is still unclear. Here, we aim to characterize the cellular states that emerge and cooperate in the wound response, using the Drosophila melanogaster wing disc as a model system. We used single-cell multi-omics profiling to derive enhancer Gene Regulatory Networks (eGRNs) from chromatin accessibility, transcription factor binding motif and gene expression signals. We identify the eGRNs being activated following a transient wound induction, and compare them with the scRNA profiles obtained from a persistent induction of the rasv12 scrib-/- oncogenic driver. We detect a small cell population in the wound that activates a senescence program that is shared with cancer cells. This population is characterized by the C/EBP-like transcription factors Irbp18, Xrp1, slow-border and vrille. Our single-cell multiome and eGRNs resource offers a new perspective on gene regulation in the normal and wounded wing disc.
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| Overall design |
Wing imaginal discs in wild-type condition or following a 40h-induction of the TNF ligand eiger (egr) in the pouch were dissected and analysed using 10x multiome scATAC + scRNA experiments
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| Contributor(s) |
Floc'hlay S, Classen A, Aerts S |
| Citation(s) |
37133250 |
| Submission date |
Jun 02, 2022 |
| Last update date |
Jun 26, 2023 |
| Contact name |
Stein Aerts |
| Organization name |
VIB-KU Leuven
|
| Department |
Department of Human Genetics / VIB Center for Brain and Disease Research
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| Lab |
Laboratory of Computational Biology
|
| Street address |
Herestraat 49
|
| City |
Leuven |
| State/province |
Flemish-Brabant |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
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| Platforms (1) |
| GPL25244 |
Illumina NovaSeq 6000 (Drosophila melanogaster) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE205401 |
Shared enhancer gene regulatory networks between wound and oncogenic programs |
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| Relations |
| BioProject |
PRJNA844964 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE205387_REW__454c70__69c6c8__Dros_rotundGAL4_GAL80ts_eiger_10x_multi_s3.barcodes.tsv.gz |
2.1 Mb |
(ftp)(http) |
TSV |
| GSE205387_REW__454c70__69c6c8__Dros_rotundGAL4_GAL80ts_eiger_10x_multi_s3.features.tsv.gz |
413.1 Kb |
(ftp)(http) |
TSV |
| GSE205387_REW__454c70__69c6c8__Dros_rotundGAL4_GAL80ts_eiger_10x_multi_s3.matrix.mtx.gz |
167.6 Mb |
(ftp)(http) |
MTX |
| GSE205387_REW__51c215__7eeed7__Dros_rotundGAL4_GAL80ts_eiger_10x_multi_s1.barcodes.tsv.gz |
2.1 Mb |
(ftp)(http) |
TSV |
| GSE205387_REW__51c215__7eeed7__Dros_rotundGAL4_GAL80ts_eiger_10x_multi_s1.features.tsv.gz |
412.4 Kb |
(ftp)(http) |
TSV |
| GSE205387_REW__51c215__7eeed7__Dros_rotundGAL4_GAL80ts_eiger_10x_multi_s1.matrix.mtx.gz |
121.0 Mb |
(ftp)(http) |
MTX |
| GSE205387_REW__e37570__709b79__Dros_rotundGAL4_GAL80ts_ctrl_10x_multi_s2.barcodes.tsv.gz |
2.1 Mb |
(ftp)(http) |
TSV |
| GSE205387_REW__e37570__709b79__Dros_rotundGAL4_GAL80ts_ctrl_10x_multi_s2.features.tsv.gz |
423.2 Kb |
(ftp)(http) |
TSV |
| GSE205387_REW__e37570__709b79__Dros_rotundGAL4_GAL80ts_ctrl_10x_multi_s2.matrix.mtx.gz |
160.8 Mb |
(ftp)(http) |
MTX |
| GSE205387_consensus_peak_set_atac.bed.gz |
2.8 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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