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Series GSE227858 Query DataSets for GSE227858
Status Public on Mar 22, 2023
Title Shared enhancer gene regulatory networks between wound and oncogenic programs [RNA]
Organism Drosophila melanogaster
Experiment type Expression 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.
 
Overall design Wild-type wing imaginal discs with induced Xrp1 expression were dissected and analysed using RNA-seq experiments
 
Contributor(s) Floc'hlay S, Uhlirova M, Classen A, Aerts S
Citation(s) 37133250
Submission date Mar 21, 2023
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
Lab Laboratory of Computational Biology
Street address Herestraat 49
City Leuven
State/province Flemish-Brabant
ZIP/Postal code 3000
Country Belgium
 
Platforms (1)
GPL30203 NextSeq 2000 (Drosophila melanogaster)
Samples (4)
GSM7109882 bulk_wing_discs_Rn1_1_ctrl
GSM7109883 bulk_wing_discs_Rn1_2_ctrl
GSM7109884 bulk_wing_discs_Xrp1_S_2_1
This SubSeries is part of SuperSeries:
GSE205401 Shared enhancer gene regulatory networks between wound and oncogenic programs
Relations
BioProject PRJNA947192

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Supplementary file Size Download File type/resource
GSE227858_RAW.tar 260.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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