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Sequencing of RNA and footprints of wildtype and RpS5b mutant Drosophila ovaries [RNA-seq]

ABSTRACT: Sequencing of RNA and footprints of wildtype and RpS5b mutant Drosophila ovaries [RNA-seq]

PROVIDER: PRJNA714408 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13961016.fastq.gz	Fastqsanger.gz
	SRR13961017.fastq.gz	Fastqsanger.gz
	SRR13961018.fastq.gz	Fastqsanger.gz
	SRR13961019.fastq.gz	Fastqsanger.gz

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Sequencing of RNA and footprints of wildtype and RpS5b mutant Drosophila ovaries

Project description:Sequencing of RNA and footprints of wildtype and RpS5b mutant Drosophila ovaries

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Sequencing of RNA and footprints of wildtype and RpS5b mutant Drosophila ovaries [RIBO-seq]

Project description:Sequencing of RNA and footprints of wildtype and RpS5b mutant Drosophila ovaries [RIBO-seq]

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Sequencing of all RNA species by next generation sequencing of wildtype and GCNAKO Drosophila ovaries

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.

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Sequencing of RNA and footprints of wildtype and RpS5b mutant Drosophila ovaries [RNA-seq]

Project description:Emerging evidence suggests that ribosome heterogeneity may have important functional consequences in the translation of specific mRNAs within different cell types and under various conditions. Ribosome heterogeneity comes in many forms including post-translational modification of ribosome proteins (RPs), lack of specific RPs, and different RP paralogs incorporation. The Drosophila genome encodes for two RPS5 paralogs, RpS5a and RpS5b. While RpS5a is expressed ubiquitously, RpS5b exhibits enriched expression in the reproductive system. Deletion of RpS5b results in female sterility marked by developmental arrest of egg chambers at stages 7-8 and posterior follicle cell (PFC) hyperplasia. Both phenotypes are caused by defects in the germline and over-expression of RpS5a can compensate it. RpS5b mutant display increased rRNA transcription and RP production, accompanied by increased protein synthesis. Loss of RpS5b leads to microtubule-based defects and mislocalization of several factors, leading failure of Notch pathway activation in PFCs. Together, our results indicate that germ cell specific expression of RpS5b promotes proper egg chamber development by regulating both ribosome homeostasis and protein trafficking during mid-oogenesis.

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Expression analysis of wildtype (OregonG) and upSET mutant ovaries.

Project description:Developmental gene expression results from the orchestrated interplay between genetic and epigenetic mechanisms. Here, we describe upSET, a transcriptional regulator encoding a SET domaincontaining protein recruited to active and inducible genes in Drosophila. However, unlike other Drosophila SET proteins associated with gene transcription, UpSET is part of an Rpd3/Sin3-containing complex that restricts chromatin accessibility and histone acetylation to promoter regions. In the absence of UpSET, active chromatin marks and chromatin accessibility increase and spread to genic and flanking regions due to destabilization of the histone deacetylase complex. Consistent with this, transcriptional noise increases, as manifest by activation of repetitive elements and off-target genes. Interestingly, upSET mutant flies are female sterile due to upregulation of key components of Notch signaling during oogenesis. Thus UpSET defines a class of metazoan transcriptional regulators required to fine tune transcription by preventing the spread of active chromatin. A six chip study using total RNA recovered from three separate dissections wild-type ovaries and three separate dissections of epic mutant ovaries. Each chip measures the expression level of 15,473 genes from Drosophila melanogaster with four 60-mer probes per target gene. Investigation of whole genome gene expression level changes in epic(e00365) mutants, compared to the wild-type strain (OregonG). The mutation was generated by the insertion of the PBac{WH}CG9007e000365 transposon. The mutants analyzed in this study are further described in Rincon-Arano H., et al 2012. in Press.

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Sequencing of RNA and footprints of wildtype and RpS5b mutant Drosophila ovaries

Project description:This SuperSeries is composed of the SubSeries listed below.

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