GEO DataSets

(Submitter supplied) we have performed mRNA-Seq studies of the larval eye and antennal primordial at multiple timepoints within the third larval instar and white prepupal stages

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9061

12 Samples

Download data: XLSX

(Submitter supplied) 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. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21306 GPL9061

13 Samples

Download data: BED, BW, XLS

(Submitter supplied) How temporal cues combine with spatial inputs to control gene expression during development is poorly understood. Here, we test the hypothesis that the Drosophila transcription factor E93 controls temporal gene expression by regulating chromatin accessibility. Precocious expression of E93 early in wing development reveals that it can simultaneously activate and deactivate different target enhancers. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9061 GPL17275

39 Samples

Download data: BED, BW, CSV, NARROWPEAK

(Submitter supplied) To elucidate endogenous gene expression profiles in germ cells at discrete but continuous differentiation stages, we developed a new experimental strategy that we named Transcriptome Analysis using Single Germline Cyst (TASC).

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9061 GPL17275

19 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9061 GPL17275

27 Samples

Download data: BW

(Submitter supplied) 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.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL17275 GPL9061

12 Samples

Download data: TXT

(Submitter supplied) eyeless (ey) is one of the most critical transcription factors for initiating the entire eye development in Drosophila. However, the molecular mechanisms through which Ey regulates target genes and pathways have not been characterized at the genomic level. Using ChIP-Seq, we generated an endogenous Ey binding profile in Drosophila developing eyes. These data sets will serve as a valuable resource for future studies on Ey and eye development.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9061

8 Samples

Download data: WIG

(Submitter supplied) The sequence read archive (SRA) contains over 52 terabases or 482 billion reads from Drosophila melanogaster (as of June 2018). These data are massively underused by the community and include 14,423 RNA-Seq samples, that is roughly 7 times the size of modENCODE. Currently the major challenge is finding high quality datasets that are suitable for inclusion in new studies. To help the community overcome this hurdle, we re-processed all D. more...

Organism:

Drosophila melanogaster

Type:

Third-party reanalysis; Expression profiling by high throughput sequencing

18 related Platforms

14423 Samples

Download data: BW, GTF, TSV, TXT

(Submitter supplied) A series of transfections was performed in Drosophila S2 cells to explore: 1) the types of target sites that Drosophila microRNAs recognize, 2) the relative functional efficacy of these sites in mediating repression, and 3) the determinants that allow some sites to have greater potency than others. 3p-seq was also performed to help reannotate and quantify the landscape of 3' UTRs in Drosophila S2 cells.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9061

10 Samples

Download data: BED, TXT

(Submitter supplied) MicroRNAs (miRNA) are small, endogenous RNAs that regulate the expression of mRNAs posttranscriptionally. To identify miRNAs that produce twin products, we sequenced these five small RNA libraries and collected other published datasets to represent a systematic coverage of the major tissue types (head, body and sexual organs) in D. melanogaster. To survey the repression effects of twin miRs on the their targets, we dissected testes from adult flies that lacked Dm310s due to a knock-out mutation (Tang, et al. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9061 GPL13304

9 Samples

Download data: FA, TXT, XLSX

(Submitter supplied) Eukaryotic genomes contain various types of small non-coding RNAs such as microRNAs (miRNAs), silencing RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs). Recent studies point to the presence of a more diverse array of uncharacterized small regulatory RNAs including those that are generated from mRNAs, rRNAs and tRNAs. To explore the possible involvement of tRNA-derived fragments (tRFs) in translational regulation, we fractionated 1 and 8h Drosophila embryos on sucrose density gradients and quantitatively measured by deep-dequencing the expression levels of the tRFs in the fractionated and unfractionated Drosophila embryonic cytosolic extracts. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9061

10 Samples

Download data: FASTQ, TXT, XLS

(Submitter supplied) Grainy head (Grh) is a conserved transcription factor (TF) controlling epithelial differentiation and regeneration. To elucidate Grh functions, we identified embryonic Grh targets by ChIP-seq and gene expression analysis. We show that Grh controls hundreds of target genes. Repression or activation correlates with the distance of Grh binding sites to the transcription start sites of its targets. Analysis of 54 Grh-responsive enhancers during development and upon wounding suggests cooperation with distinct TFs in different contexts. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9061

3 Samples

Download data: BED, FASTA

(Submitter supplied) Seminal fluid proteins (Sfps) can have significant effects on female behaviour and physiology. In Drosophila melanogaster a single Sfp, sex peptide (SP), triggers a remarkably diverse array of fundamentally important responses. It increases female fecundity, juvenile hormone (JH) production, antimicrobial peptide production and feeding rates, whilst decreasing sexual receptivity. Although these features are expected to leave a strong genomic signature, previous studies indicated that Sfps affect the expression of relatively modest numbers of genes. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9061

8 Samples

Download data

(Submitter supplied) We identify a temporal cascade of ecdysone-inducible transcription factor gene expression during Drosophila wing development. This temporal cascade corresponds with dynamic changes in chromatin accesibility during wing development. We hypothesized that these temporally regulated transcription factors may coordinate these dynamic open chromatin changes. To test this, we investigate the ecdysone-inducible transcription factor, E93, which we determine is required for coordinating transitions in developmental stage by regulating chromatin accesibility of cis-regulatory elements.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL9061 GPL17275

24 Samples

Download data: BED, BW, TXT, XLSX

(Submitter supplied) Piwi-Interacting RNAs (piRNAs) are central components of the piRNA pathway, which directs transposon silencing and guarantees genome integrity in the germ cells of several metazoans. In Drosophila, piRNAs are produced from discrete regions of the genome termed piRNA clusters, whose expression relies on the RDC complex comprised of the core proteins Rhino, Deadlock and Cutoff. To date, the RDC complex has been exclusively implicated in the regulation of the piRNA loci. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9061

17 Samples

Download data: BED, TXT

(Submitter supplied) Transcriptional analysis of Drosophila CNS midline cells provides a useful system for studying transcriptional regulation at the genomic level due to a well-characterized set of midline-expressed genes and in vivo-validated enhancers. To investigate how access to regulatory information is controlled during midline cell development, we performed FAIRE-seq on FACS-purified midline cells. We find that regions of the genome with a strong midline FAIRE peak and weak whole-embryo FAIRE peak (“midline-enriched”) often correspond to midline enhancers near a midline-expressed gene and provides a useful predictive tool. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9061 GPL13304

5 Samples

Download data: BED, WIG

(Submitter supplied) Because maturing oocytes and early embryos lack transcription, posttranscriptional regulatory processes must control their development. To better understand this control, we profiled translational efficiencies and poly(A)-tail lengths throughout Drosophila oocyte maturation and early embryonic development. The correspondence between translational-efficiency changes and tail-length changes indicated that tail-length changes broadly reshape translational activity until gastrulation, when this coupling disappears. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL9061 GPL17275

42 Samples

Download data: TXT

(Submitter supplied) We report the binding of MSL1 protein in male, female and mof2 mutant samples of Drosophila melanogaster and Drosophila virilis

Organism:

Drosophila virilis; Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

10 Samples

Download data: BW

(Submitter supplied) Hi-C analysis of two Drosophila male cell lines, combined with 4C-seq of frequent long-range contacts between HAS.

Organism:

Drosophila melanogaster

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

100 Samples

Download data: BED, BIGWIG, BW, TXT

(Submitter supplied) Precise gene expression is a fundamental aspect of organismal function and depends on the combinatorial interplay of transcription factors (TFs) with cis‐regulatory DNA elements. While much is known about TF function in general, our understanding of their cell type‐specific activities is still poor. To address how widely expressed transcriptional regulators modulate downstream gene activity with high cellular specificity, we have identified binding regions for the Hox TF Deformed (Dfd) in the Drosophila genome. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9061

2 Samples

Download data: CSV