Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1179511 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31154200_1.fastq.gz | Fastqsanger.gz | |||
| SRR31154200_2.fastq.gz | Fastqsanger.gz | |||
| SRR31154201_1.fastq.gz | Fastqsanger.gz | |||
| SRR31154201_2.fastq.gz | Fastqsanger.gz | |||
| SRR31154202_1.fastq.gz | Fastqsanger.gz |
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Project description:We report the changes in chromatin accessibility associated with regeneration in wing imaginal discs at two developmental timepoints during L3. Wing discs were ablated using tissue-specific expression of the pro-apoptotic gene eiger at an early timepoint (day 7) when the discs retain high regenerative capacity and at a late time point (day 9) when regenerative capacity has significantly declined. ATAC-seq was performed on these discs after 40 hr of ablation and compared to identically staged unablated discs. We detect 14,142 open chromatin peaks after merging overlapping peaks from 3 biological repeats of all 4 conditions. Of these, 349 change significantly (log2fc>0.5, p<0.1) either opening or closing upon damage in early L3 discs, while only 55 open or close in late L3 discs. We describe two consequential groups of peak changes, those that are damage responsive (DR) in early L3 (222 peaks) and those that are maturity silenced (MS), open in early damaged L3 and closed in late damaged L3 (729 peaks). 28 peaks fall in the overlap of these two groups.
2020-06-11 | GSE140755 | GEO
Project description:Regeneration of fragmented Drosophila imaginal discs occurs in an epimorphic manner, involving local cell proliferation at the wound site. Following disc fragmentation, cells at the wound site activate a restoration program through wound healing, regenerative cell proliferation and repatterning of the tissue. However, the interplay of signaling cascades, driving these early reprogramming steps, is not well understood. Here we profiled the transcriptome of regenerating cells in the early phase within twenty-four hours after wounding. We found that JAK/STAT signaling becomes activated at the wound site and promotes regenerative cell proliferation in cooperation with Wingless (Wg) signaling. In addition, we demonstrated that the expression of Drosophila insulin-like peptide 8 (dilp8), which encodes a paracrine peptide to delay the onset of pupariation, is controlled by JAK/STAT signaling in early regenerating discs. Our findings suggest that JAK/STAT signaling plays a pivotal role in coordinating regenerative disc growth with organismal developmental timing. In order to analyze transcriptome change in early regenerating imaginal disc, Drosophila prothorasic leg discs were fragmented (to anterior one-quarter or posterior three-quarters) and cultured ex vivo in adult fly abdomen. Regenerating cells in early regeneration phase (at 12 or 24 hours after wounding) were subjected to transcriptome profiling with Affymetrix microarrays. For control samples, the corresponding regions of uncut-cultured discs and uncut-uncultured discs were used.
2015-04-10 | E-GEOD-54868 | biostudies-arrayexpress
Project description:The Drosophila genitalia develop from an imaginal disc that is patterned during the larval period and undergoes morphogenesis during the pupal period. Although the genetic hierarchy that controls sexual identity in Drosophila is well characterized, the downstream genes that effect sexually dimorphic development of the genitalia are largely unknown. We used microarrays to profile gene expression in female and male genital imaginal discs at three time points during development: late third-instar larvae (L3), pupae approximately 6 hours after puparium formation (P6) and pupae approximately 20 hours after puparium formation (P20). We identified genes that are sex-differentially expressed in the developing genital disc, including three genes encoding transcription factors that are expressed in the genital disc of one sex but not the other. Through genetic analysis, we showed how the master regulator of sexual identity, Doublesex, limits expression of each of these three genes to one sex. We also determined which genital structures fail to develop properly in the absence of each of the three genes.
2011-02-25 | GSE23344 | GEO
Project description:The systemic response to injury in Drosophila melanogaster is characterized by the activation of specific signaling pathways that facilitate the regeneration of wounded tissue and help coordinate wound healing with organism growth. The mechanisms by which damaged tissues influence the development and function of peripheral non-injured tissues is not fully understood. Injury was induced in early third instar larvae via temperature-dependent cell death in wing imaginal discs. Microarray analysis using RNA isolated from injured and control was used to identify genes underlying the systemic injury response. We identified 150 genes which were differentially expressed in response to localized cell death in wing imaginal discs. Upregulated genes were associated biological processes including carnitine biosynthesis, signal transduction and regulation of oxidoreductase activity while terms associated with downregulated genes included wound healing, imaginal disc-derived wing hair outgrowth, and regulation of glutamatergic synaptic transmission. Pathway analysis revealed that wing disc damage led to changes in fatty acid, cysteine, and carnitine metabolism. One gene, 14-3-3ζ, which encodes a known regulator of Ras/MAPK signaling was identified as a potential regulator of transdetermination during tissue regeneration. Our results raise the possibility that immune function and cell proliferation during wing disc repair and regeneration in Drosophila may require the sulfur amino acid cysteine and its’ metabolites, taurine and glutathione, similar to what has been reported during tissue repair in mammals. Further, it seems likely that imaginal disc damage stimulates the mobilization of fatty acids to support the energetically demanding process of tissue regeneration. The roles of additional genes that are differentially regulated following imaginal disc injury remain to be elucidated.
2017-09-30 | GSE94938 | GEO
Project description:We report on changes in gene expression resulting from the ecdysone-directed broad-based transcriptional regulatory hierarchy in Drosophila melanogaster leg imaginal discs by comparing expression in white1118 third-instar larvae (-18 hrs relative to pupariation) and white prepupae (0 hrs) to examine the transcriptional effects of the late larval ecdysone pulse, as well comparing expression in white1118 and broad5 white prepupal leg imaginal discs to examine the transcriptional effects of the early ecdysone responder, broad. Using this approach, we were able to identify critical leg disc elongation genes that are differentially regulated in broad mutants
2019-11-13 | GSE140248 | GEO
Project description:The Drosophila genitalia develop from an imaginal disc that is patterned during the larval period and undergoes morphogenesis during the pupal period. Although the genetic hierarchy that controls sexual identity in Drosophila is well characterized, the downstream genes that effect sexually dimorphic development of the genitalia are largely unknown. We used microarrays to profile gene expression in female and male genital imaginal discs at three time points during development: late third-instar larvae (L3), pupae approximately 6 hours after puparium formation (P6) and pupae approximately 20 hours after puparium formation (P20). We identified genes that are sex-differentially expressed in the developing genital disc, including three genes encoding transcription factors that are expressed in the genital disc of one sex but not the other. Through genetic analysis, we showed how the master regulator of sexual identity, Doublesex, limits expression of each of these three genes to one sex. We also determined which genital structures fail to develop properly in the absence of each of the three genes. Drosophila female or male genital discs were dissected at the L3, P6 or P20 time points, total RNA was extracted, and labeled cDNA was produced for hybridization to Affymetrix microarrays. To aid in identifying genital discs, and thereby to avoid loss or contamination of tissue, we used animals expressing GFP in all imaginal discs (esgGAL4.B, UAS-GFP.nls/CyO). To collect discs of specific developmental ages, short-duration sex-nonspecific morphological features were used. L3 discs were dissected from wandering third-instar larvae and sexed by gonad size. For the two pupal time points, each sex-sorted larva was observed until it reached the white prepupa stage (0 hours after puparium formation, APF), which lasts 15-20 minutes. This short duration improves synchronization of the following stages. An air bubble forms mid-dorsally on the puparium at around 4 hours APF, peaks in size at 6-6.5 hours APF and disappears at 9-11 hours APF. We therefore used this morphological feature to collect P6 samples, rather than merely timing 6 hours since the white prepupa. Each animal was observed every 20 minutes from 5 hours APF, until peak bubble size was evident, at which time its genital disc was dissected. We followed a similar protocol for P20. We noted that GFP expression in an oval patch in the eye disc becomes faintly visible at around 20 hours APF. We observed each pupa every 20 minutes from 18 hours APF, until GFP appeared in the eye, at which time its genital disc was dissected. Morphologies of P6 and P20 discs collected this way showed little within-sex variation. For each combination of sex and time point, four biological replicates were performed.
2011-02-25 | E-GEOD-23344 | biostudies-arrayexpress
Project description:Growth of the drosophila eye imaginal discs is controlled by the activation of Notch in the dorsal-ventral boundary. Overexpression in the eye disc of the Notch ligand Delta together with lola and pipsqueak from the GS(2)88A8 line induces tumoral growth. We used microarray to analyze the expression profile of tumoral discs. Antennal-eye discs of Drosophila L3 larvae were selected for RNA extraction and hybridization on Affymetrix microarrayas. Two genetic conditions were analyzed: tumoral eye discs (ey-Gal4 GS(2)88A8 UAS-Dl) and control eye discs (GS(2)88A8 UAS-Dl). Three different biological replicates of each condition, each one consisting on 300 hundred pairs of eye discs, were analyzed.
2012-02-20 | E-GEOD-35471 | biostudies-arrayexpress
Project description:Atonal is a proneural transcription factor expressed in the Drosophila eye imaginal discs. To characterize the putative targes of Atonal in the eye discs we have used an endogenously GFP-tagged version of atonal to immunoprecipate disc samples with anti-GFP antibodies
2019-10-09 | GSE138553 | GEO
Project description:Genomic enhancers regulate spatio-temporal gene expression by recruiting specific combinations of transcription factors (TFs). When TFs are bound to active regulatory regions, they displace canonical nucleosomes, making these regions biochemically detectable as nucleosome-depleted regions or accessible/open chromatin. Here we ask whether open chromatin profiling can be used to identify the entire repertoire of active promoters and enhancers underlying tissue-specific gene expression during normal development and oncogenesis in vivo. To this end, we first compare two different approaches to detect open chromatin in vivo using the Drosophila eye primordium as a model system: FAIRE-seq, based on physical separation of open versus closed chromatin; and ATAC-seq, based on preferential integration of a transposon into open chromatin. We find that both methods reproducibly capture the tissue-specific chromatin activity of regulatory regions, including promoters, enhancers, and insulators. Using both techniques, we screened for regulatory regions that become ectopically active during Ras-dependent oncogenesis, and identified 3778 regions that become (over-)activated during tumor development. Next, we applied motif discovery to search for candidate transcription factors that could bind these regions and identified AP-1 and Stat92E as key regulators. We validated the importance of Stat92E in the development of the tumors by introducing a loss of function Stat92E mutant, which was sufficient to rescue the tumor phenotype. Additionally we tested if the predicted Stat92E responsive regulatory regions are genuine, using ectopic induction of JAK/STAT signaling in developing eye discs, and observed that similar chromatin changes indeed occurred. Finally, we determine that these are functionally significant regulatory changes, as nearby target genes are up- or down-regulated. In conclusion, we show that FAIRE-seq and ATAC-seq based open chromatin profiling, combined with motif discovery, is a straightforward approach to identify functional genomic regulatory regions, master regulators, and gene regulatory networks controlling complex in vivo processes. FAIRE-Seq in Drosophila wild type eye-antennal imaginal discs (2 wt strains); ATAC-Seq in Drosophila wild type eye-antennal imaginal discs (3 wt strains) ; FAIRE-Seq in Drosophila Ras/Scrib induced eye disc tumors (1 early and 1 late); ATAC-Seq in Drosophila Ras/Scrib induced eye disc tumors (1 early and 1 late); ATAC-Seq in Drosophila eye discs with Unpaired over-expression (2 biological replicates); CTCF ChIP-seq in Drosophila eye discs; ChIP-seq input in Drosophila eye discs
2015-02-13 | E-GEOD-59078 | biostudies-arrayexpress
Project description:Regeneration of fragmented Drosophila imaginal discs occurs in an epimorphic manner, involving local cell proliferation at the wound site. Following disc fragmentation, cells at the wound site activate a restoration program through wound healing, regenerative cell proliferation and repatterning of the tissue. However, the interplay of signaling cascades, driving these early reprogramming steps, is not well understood. Here we profiled the transcriptome of regenerating cells in the early phase within twenty-four hours after wounding. We found that JAK/STAT signaling becomes activated at the wound site and promotes regenerative cell proliferation in cooperation with Wingless (Wg) signaling. In addition, we demonstrated that the expression of Drosophila insulin-like peptide 8 (dilp8), which encodes a paracrine peptide to delay the onset of pupariation, is controlled by JAK/STAT signaling in early regenerating discs. Our findings suggest that JAK/STAT signaling plays a pivotal role in coordinating regenerative disc growth with organismal developmental timing.
2015-04-10 | GSE54868 | GEO