Transcriptome analysis in transgenerational epigenetic inheritance
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE222543 | GEO | 2024/01/05
REPOSITORIES: GEO
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Project description:Wild-type Drosophila melanogaster expressing nuclear GFP-KASH fusion protein in photoreceptors for cell type-specific gene expression profiling (Rh1-Gal4>UAS-GFPKASH ; Genotype = w1118;; P{w+mC=[UAS-GFP-Msp300KASH}attP2, P{ry+t7.2=rh1-GAL4}3, ry506) were raised in 12:12h light:dark cycle at 25°C. Flies were aged for 10 or 40 days post-eclosion, and eyes were harvested from male flies for global quantitative proteomic analysis. Significantly changed proteins were identified that may contribute to age-associated retinal degeneration and loss of visual function in the aging Drosophila eye.
2021-07-23 | PXD027090 | Pride
Project description:When misexpressed in late Drosophila prepupae, the transcription factor Senseless (Sens) blocks death of the larval salivary glands that normally occurs in the early pupa. The aim of the experiment was to identify genes responding to Sens that might mediate the effect of the protein on cell death and other biological processes. The yeast transcription factor GAL4, expressed from a heat-inducible transgene (P{GAL4-Hsp70.PB}89-2-1), was used to drive expression of Sens from a UAS-sens transgene. After crossing the GAL4 and UAS lines, expression of GAL4 was induced by a 30-min heat shock treatment (37 °C) of the progeny at 9 hours after puparium formation. Salivary glands were dissected at 14 hours after puparium formation and RNA isolated for microarray analysis with Affymetrix GeneChips. Control samples were obtained from animals treated the same way carrying one copy of the GAL4 transgene (progeny of a cross between flies of the P{GAL4-Hsp70.PB}89-2-1 and w1118 strains) and w1118 animals. The microarray data identified several genes associated with programmed cell death, including caspase genes, which respond to Sens. In addition, the data show that many Drosophila genes respond to the yeast transcription factor GAL4 in a UAS-independent manner. To identify target genes of Sens that are of biological relevance, gene expression patterns in the presence of Sens were compared to gene expression patterns in both the presence and the absence of GAL4. This comparison revealed that Sens seems to preferentially downregulate targets that are upregulated by GAL4, suggesting that these genes may not necessarily constitute true transcriptional targets of Sens. Keywords: ectopic expression experiment
2008-05-29 | GSE8619 | GEO
Project description:Many protein complexes are involved in gene regulation during Drosophila spermatogenesis. tplus3a and tplus3b code for Plus3 domain proteins and are enriched in spermatocytes. Male flies ∆tplus3a/b carrying deletions of both genes in trans to deficiency Df(2L)BSC151 show severely reduced fertility. tbrd-1 is known to regulate hundreds of genes during spermatogenesis in cooperation with tTAFs. To gain more insight into the regulatory mechanisms during spermatogenesis we used RNA from testes of ∆tplus3a/b/Df(2L)BSC151 and tbrd-11 mutant flies for RNAseq in comparison to w1118 wild-typic control. RNA was isolated with Trizol from 200 Testes dissected from w1118, homozygous tbrd-11 mutants or ∆tplus3a/b/Df(2L)BSC151. After DNAse I digestion RNA was purified and RNAseq was performed in three replicates. Genotype Description: w1118: wild-typic control tbrd-11: homozygous tbrd-11 mutants (knock-out through P{EPgy2}tbrd-11, as described in Leser et al., 2012) ∆tplus3a/b/Df(2L)BSC151: CRISPR/Cas9 deletion mutants, representing knock-out of both tplus3 and tplus3b. Male flies y1cho2v1;∆tplus3a/b/CyO were crossed with virgin females w1118;Df(2L)BSC151/CyO. Male offspring with w1118;∆tplus3a/b/Df(2L)BSC151 were used for RNAseq.
2019-11-04 | E-MTAB-7013 | biostudies-arrayexpress
Project description:To detect dysregulated genes upon overexpression of the functional smad suppressing element (fuss) in Drosophila melanogaster, we overexpressed fuss with the GMR-Gal4 line in developing eye discs and with the nub-Gal4 driverline in developing wing discs. The offspring of crossings of the driver lines GMR-Gal4 or nub-Gal4 with w1118 were used as controls. Libraries were generated from total RNA and sequenced on a Illumina HiSeq 1000. Via differential gene expression analysis we discovered the genes which are dysregulated by fuss overexpression compared to controls.
2022-01-05 | GSE165738 | GEO
Project description:During Drosophila melanogaster oogenesis, the JAK/STAT and EGFR pathways are both required to specify a population of somatic epithelial cells called the posterior follicle cells (PFCs). The PFCs are important because they generate a signal at mid-oogenesis that is required to establish the embryonic axes. To identify novel PFC-expressed transcripts, egg chambers containing ectopic PFCs were generated and microarrays were then used to identify upregulated transcripts. To generate ectopic PFCs, GAL80TS / CyO ; UAS-Upd, UAS-λtorpedo/TM6B flies were crossed to GR1-GAL4 flies to obtain the genotype GAL80TS/+ ; GR1-GAL4/UAS-Unpaired, UAS-λtorpedo. Sibling females of genotype GAL80TS/+ ; GR1-GAL4/TM6B were dissected as controls.
2018-10-30 | GSE118881 | GEO
Project description:When misexpressed in late Drosophila prepupae, the transcription factor Senseless (Sens) blocks death of the larval salivary glands that normally occurs in the early pupa. The aim of the experiment was to identify genes responding to Sens that might mediate the effect of the protein on cell death and other biological processes. The yeast transcription factor GAL4, expressed from a heat-inducible transgene (P{GAL4-Hsp70.PB}89-2-1), was used to drive expression of Sens from a UAS-sens transgene. After crossing the GAL4 and UAS lines, expression of GAL4 was induced by a 30-min heat shock treatment (37 °C) of the progeny at 9 hours after puparium formation. Salivary glands were dissected at 14 hours after puparium formation and RNA isolated for microarray analysis with Affymetrix GeneChips. Control samples were obtained from animals treated the same way carrying one copy of the GAL4 transgene (progeny of a cross between flies of the P{GAL4-Hsp70.PB}89-2-1 and w1118 strains) and w1118 animals. The microarray data identified several genes associated with programmed cell death, including caspase genes, which respond to Sens. In addition, the data show that many Drosophila genes respond to the yeast transcription factor GAL4 in a UAS-independent manner. To identify target genes of Sens that are of biological relevance, gene expression patterns in the presence of Sens were compared to gene expression patterns in both the presence and the absence of GAL4. This comparison revealed that Sens seems to preferentially downregulate targets that are upregulated by GAL4, suggesting that these genes may not necessarily constitute true transcriptional targets of Sens. Experiment Overall Design: Experimental RNA samples were obtained in 3 biological replicates from sens-expressing salivary glands (SG_sens_14APF_rep1, SG_sens_14APF_rep2, SG_sens_14APF_rep3) and compared to control samples obtained from GAL4-expressing salivary glands (SG_1P{hsGAL4}89(S)_14APF_rep1) and non-GAL4-expressing salivary glands (SG_w1118_14APF_rep1, SG_w1118_14APF_rep2). All samples were compared using dChip and normalized to the same baseline array (median intensity 150).
2008-06-19 | E-GEOD-8619 | biostudies-arrayexpress
Project description:To determine functions of circMbl in brain in vivo we generated genetically encoded shRNA directed against individual circRNA-specific back-spliced junctions. We analyzed gene expression by 3' RNA-seq from control (actin-Gal4) and flies expressing the shRNA under the control of a constitutive driver (actin-Gal4; circRNA KD).
2023-12-01 | GSE163797 | GEO
Project description:The yeast transcription factor GAL4 has been reported to cause cell death and to have other biological effects when expressed in Drosophila (Kramer and Staveley, 2003: Genet. Mol. Res. 2, 43; Rezaval et al., 2007: Eur. J. Neurosci. 25, 683). Using heat-shock-induced expression of GAL4 to drive expression of a UAS-senseless responder gene in transcriptional profiling experiments, we found that the underlying cause of these effects might be a genomic response to GAL4. To further characterize this response and to account for GAL4-independent changes caused by the transgene integration, GAL4 was expressed from two copies of the transgene in two independent lines, P{GAL4-Hsp70.PB}89-2-1 (short P{hs-GAL4}89) and P{hs-GAL4}X1. In addition, GAL4 was expressed from only one copy of the transgene in P{hs-GAL4}89 prepupae to account for the dosage dependence of observed effects. Prepupae carrying the hs-GAL4 transgenes were subjected to a 30-min heat shock treatment (37 °C) at 9 hours after puparium formation. RNA was isolated from salivary glands dissected from these and similarly treated w1118 control animals at 14 hours after puparium formation and subjected to microarray analysis with Affymetrix GeneChips. The microarray data identified an overlapping set of 1,009 genes that showed an at least 1.5-fold change in expression in both of the GAL4-expressing lines, defining a core set of GAL4-responsive genes in the salivary glands. This set includes genes involved in the control and execution of programmed cell death and in other important regulatory pathways. Experiment Overall Design: Experimental RNA samples were obtained from GAL4-expressing salivary glands of the line P{hs-GAL4}X1 in 3 biological replicates (SG_P{hsGAL4}X1_14APF_rep1, SG_P{hsGAL4}X1_14APF_rep2, SG_P{hsGAL4}X1_14APF_rep3); of the line P{hs-GAL4}89 in one replicate (SG_P{hsGAL4}89_14APF_rep1); of animals carrying only one copy of P{hs-GAL4}89 in one replicate (SG_1P{hsGAL4}89_14APF_rep1). The samples were compared to control samples obtained in two biological replicates from the salivary glands of w1118 control animals (SG_w1118(2)_14APF_rep1, SG_w1118(2)_14APF_rep2). All samples were compared using dChip and normalized to the same baseline array (median intensity 145). Statistical analysis of differences between the P{hs-GAL4}X1 and w1118 samples was carried out using GeneSpring (Agilent Technologies) and a false discovery rate (FDR) cutoff of 0.05.
2008-06-19 | E-GEOD-8620 | biostudies-arrayexpress
Project description:Parental flies (y1v1;P{TRiP.JF01138}attP2 and y1w*;P{Act5C-GAL4}25FO1/CyO,y+) were mated to obtain progeny with genotypes for ubiquitous DmSTING RNAi and sibling controls. 2-7 day old flies were used for all infections. 23 nl of listeria monocytogenes (strain 10403S) at 1e7 CFU/ml was injected intrathoracically. Mock inoculation was performed with PBS. Whole flies were homogenized 24 h post-infection.
2018-06-19 | GSE90442 | GEO
Project description:To test whether other genes were being silenced in the Cyp6g1 knockdown strain due to off-target RNAi effects, and whether other gene expression changes were contributing to the altered susceptibility to imidacloprid in these knockdown flies. A comparison between w;Act5C-GAL4/CyO; UAS:RNAi_Cyp6g1Hp2/TM3Sb and the genetic control w;Act-GAL4/CyO;+/TM3Sb was performed. Ten 2-3 day old adult males or females were transferred to sugar-agar plates and then collected at various time points (0, 2, 5, 8 hours). The RNA samples for up to three independent experiments per timepoint for each genotype were then pooled, in equal concentrations, before hybridisation to the Affymetrix Drosophila GeneChip 1. As a preliminary analysis provided evidence for assuming that there is no interaction between genotype and duration in the sugar-agar plate, the knockdown and control chips for each of the five timepoints provided some degree of replication for the comparison between the knockdown flies and control flies. Differential expression that was consistently observed between knockdown and control over each of the five timepoints was regarded as providing evidence of a genuine difference.
2011-02-17 | GSE27344 | GEO