RNA sequencing of nos-gal4>phf7ey Drosophila ovaries
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ABSTRACT:
PROVIDER: PRJNA631517 | ENA |
REPOSITORIES: ENA
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Project description:Next generation sequencing of mRNA for nos-gal4>phf7ey Drosophila ovaries
2020-08-28 | GSE150213 | GEO
Project description:Purpose: To identify significantly different individual mRNA species or genetic pathways in the GCNAKO mutant sample when compared to the wildtype sample. GCNA is encoded by CG14814 (Flybase ID: FBgn0023515). Method: Total RNA was extracted using the Qiagen miRNEasy kit, followed by on column DNAse digest using the Qiagen DNAse digest kit. We used the miRNEasy kit to ensure collection of small RNA species as well as total RNA. RNA was collected from three independent bological replicates of freshly dissected Drosophila ovaries ( 100 ovaries per replicate), collected from 1-3 day old female Drosophila. Ovaries were flash frozen in liquid nitrogen after dissection to preserve the RNA species and prevent degradation. RNAse free conditions were maintained throughout the extraction protocol. RNA quality was tested by the sequencing core before sequencing the RNA.
2019-10-22 | GSE127220 | GEO
Project description:The Drosophila piRNA pathway provides an RNA-based immune system that defends the germline genome against selfish genetic elements. Two inter-related branches of the piRNA system exist: somatic cells that support oogenesis only employ Piwi, whereas germ cells utilize a more elaborated pathway centered on the three gonad-specific Argonaute proteins Piwi, Aubergine, and Argonaute3. While several key factors of each branch have been identified, our current knowledge is insufficient to explain the complex workings of the piRNA machinery. Here, we report a reverse genetic screen spanning the ovarian transcriptome in an attempt to uncover the full repertoire of genes required for piRNA-mediated transposon silencing in the female germline. Our screen reveals new key factors of piRNA-mediated transposon silencing, including the novel piRNA biogenesis factors, CG2183 (GASZ) and Deadlock. Last, our data uncovers a previously unanticipated set of factors preferentially required for repression of different transposons types. Examination of total RNA levels from nos-GAL4 or tj-GAL4 driven UAS-dsRNA knockdowns of control genes and piRNA pathway components in ovaries of Drosophila melanogaster by deep sequencing (using Illumina HiSeq2000).
2013-05-10 | E-GEOD-46100 | biostudies-arrayexpress
Project description:Escort cells (ECs) in the Drosophila ovaries showed important functions in modulate germline cysts differentiation, as germline cysts differentiation niche, yet their subtypes and functions to germline cysts were still little known. Through single cell RNA-sequencing analysis, here we provide a comprehensive analysis of cellular diversity and functions of ECs in adult Drosophila germariums. We identify 2 EC subtypes with different gene expression and functions, further tested through EC subtypes-specific gene RNAi. Our single-cell data should greatly facilitate understanding of the functions of ECs as differentiation niche.
2020-12-09 | GSE141701 | GEO
Project description:Targeted DamID (TaDa) measures gene expression using a DNA adenine methyltransferase (Dam) fused to RNA polymerase II (Dam Pol II) to methylate DNA as the genome is transcribed (Southall, Gold et al. 2013, PMID: 23792147). Here we use traditional Illumina RNA-Seq to determine if a cell’s expression profile is affected by Dam Pol II expression. Twenty-four hours prior to collection, we ubiquitously drove UAS Dam or UAS Dam Pol II using a tubulin (tub) GAL4 regulated by a temperature sensitive tub GAL80[ts] (McGuire et al. 2003, PMID: 14657498) in adult Drosophila melanogaster (taxon: 7227) whole males, whole females, testes, and ovaries.
2018-06-13 | GSE115694 | GEO
Project description:Compare the distribution of H3K4me3 between two experimental conditions (WT and Germ cell specific Lid KD) in Drosophila ovaries
2019-12-11 | GSE133202 | 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. Keywords: ectopic expression experiment
2008-05-29 | GSE8620 | GEO
Project description:Purpose: To analysis Ova impact on transcription in Drosophila ovaries by mRNA-seq and small RNA-seq Methods: mRNA-seq and small RNA-seq of RNA extracted from Drosophila ovaries Results: Ova has no obvious impact on protein coding genes expression or piRNA biogenesis.
2019-01-14 | GSE104924 | GEO
Project description:Comparison of transcript abundance between control (untreated) and methotrexate treated S3 Drosophila cells and ovaries disected from female flies. Keywords: Stress response
2005-10-22 | GSE3495 | GEO
Project description:H3K27me3 profiles using Cleavage under targets and Release using nuclease (Cut&Run) in control and KD Drosophila melanogaster ovaries. We examined the impact on chromatin profiles in Drosophila melanogaster ovaries in which the lid, the Sin3a, the Snr1 or the mod(mdg4) gene have been selectively knocked down by tissue-specific shRNA expression. We additionally explored H3K27me3 and H3K9me3 in control and dhd mutant ovaries either carrying or not a transgene.
2021-12-10 | GSE174250 | GEO