GEO DataSets

(Submitter supplied) 3D genome folding plays a fundamental role for the regulation of developmental genes by facilitating or constraining chromatin interactions between cis-regulatory elements (CREs). Polycomb response elements (PREs) are a specific kind of CREs involved in the memory of transcriptional states in Drosophila melanogaster. PREs act as nucleation sites for Polycomb group (PcG) proteins, which deposit the repressive histone mark H3K27me3, leading to the formation of a class of topologically associating domain (TADs) called Polycomb domains. more...

Organism:

Drosophila melanogaster

Type:

Other

Platforms:

GPL32218 GPL25244

62 Samples

Download data: BIGWIG, TAR, TXT

(Submitter supplied) Alternative splicing (AS) generates large amounts of RNA isoforms and dramatically increases the complexities of transcriptomes and proteomes. However, it remains unclear how RNA structures contribute to AS regulation. Here, we systematically search transcriptomes for secondary structures with concealed branch-sites (BSs) in the alternatively spliced introns and predict thousands from six organisms, of which many are evolutionarily conserved. more...

Organism:

Drosophila melanogaster; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL20795 GPL23702

29 Samples

Download data: TXT

(Submitter supplied) Mono-methylation of Lysine 20 of histone H4 (H4K20me1) is catalyzed by Set8 and thought to play important roles in many aspects of genome function that are mediated by H4K20me-binding proteins. We interrogated this model in a developing animal by comparing in parallel the transcriptomes of Set8null, H4K20R/A, and l(3)mbt mutant Drosophila melanogaster. We found that the gene expression profiles of H4K20A and H4K20R larvae are markedly different than Set8null larvae despite similar reductions in H4K20me1. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

47 Samples

Download data: TXT

(Submitter supplied) Mono-methylation of Lysine 20 of histone H4 (H4K20me1) is catalyzed by Set8 and thought to play important roles in many aspects of genome function that are mediated by H4K20me-binding proteins. We interrogated this model in a developing animal by comparing in parallel the transcriptomes of Set8null, H4K20R/A, and l(3)mbt mutant Drosophila melanogaster. We found that the gene expression profiles of H4K20A and H4K20R larvae are markedly different than Set8null larvae despite similar reductions in H4K20me1. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30203

8 Samples

Download data: BED, BW

(Submitter supplied) Mono-methylation of Lysine 20 of histone H4 (H4K20me1) is catalyzed by Set8 and thought to play important roles in many aspects of genome function that are mediated by H4K20me-binding proteins. We interrogated this model in a developing animal by comparing in parallel the transcriptomes of Set8null, H4K20R/A, and l(3)mbt mutant Drosophila melanogaster. We found that the gene expression profiles of H4K20A and H4K20R larvae are markedly different than Set8null larvae despite similar reductions in H4K20me1. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30203

27 Samples

Download data: BED, BW

(Submitter supplied) Adult mosquitoes were fed blood containing 1e7 PFU WNV (kunjin strain) containing +/- 170 pM bovine insulin for 24 h. We then performed gene expression profiling analysis using data obtained from RNA-seq.

Organism:

Culex quinquefasciatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34558

16 Samples

Download data: TXT

(Submitter supplied) This study investigates immune priming effects associated with granulocytes in crickets through a comprehensive analysis. Kaplan-Meier survival analysis reveals a significant contrast in survival rates, with the heat-killed Bacillus thuringiensis (Bt)-primed group (B-1) exhibiting an impressive ~80% survival rate compared to the PBS buffer-primed group (A-1) with only ~10% survival 60 hours post live Bt infection. more...

Organism:

Gryllus bimaculatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34421

12 Samples

Download data: FASTA, XLSX

(Submitter supplied) This micro-array helps establish Toll activated-genes dampened by miRNAs in Drosophila melanogaster.

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL16820

12 Samples

Download data: TAB, TXT

(Submitter supplied) Understanding the molecular determinants of the mosquitoes’ competence to host the viruses holds promise to prevent their transmission. We performed transcriptomic analysis with data obtained from RNA-seq of dengue- or naïve- infected mosquitoes on day 1, 2, and 7 post infections

Organism:

Aedes aegypti

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28657

18 Samples

Download data: XLSX

(Submitter supplied) Female adult spongy moths vary in their flight capacity depending upon their origin and subspecies. Asian spongy moth (Lymantria dispar asiatica) females (such as the RM strain here) can fly whereas European spongy moth (Lymantria dispar dispar) females cannot (such as the CT strain here). We hypothesized that the genetic origins of these differences in flight capacity would be reflected in differences in gene expression during metamorphosis (the pupal stage). more...

Organism:

Lymantria dispar dispar; Lymantria dispar asiatica

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29180 GPL29179

30 Samples

Download data: FA, TXT

(Submitter supplied) It has long been proposed that cell competition functions to remove precancerous clones. A classical model is the removal of polarity-deficient clones such as the scribble (scrib) mutant clones in Drosophila imaginal discs. The activation of Ras, Yki or Notch signaling robustly reverses the scrib mutant clonal fate from elimination to tumorous growth. Using single-cell transcriptomics techniques to profile wing imaginal discs harboring the scrib mutant clones in combination with different signals, we found that a critical converging point downstream of Ras, Yki and Notch signals is the upregulation of Upd2, which is necessary to promote tumorous growth. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21306

8 Samples

Download data: CSV

(Submitter supplied) DNA methylation and gene expression in response to the loss of care for 30 generations in N. Vespilloides

Organism:

Nicrophorus vespilloides

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL20831

60 Samples

Download data: COV, CSV

(Submitter supplied) Although introns are typically tens to thousands of nucleotides, there are notable exceptions. In flies as well as humans, a small number of genes contain introns that are more than 1000 times larger than typical introns, exceeding hundreds of kilobases (kb) to megabases (Mb). It remains unknown why gigantic introns exist and how cells overcome the challenges associated with their transcription and RNA processing. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

9 Samples

Download data: TXT

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

Organism:

Drosophila melanogaster; Drosophila simulans; Drosophila melanogaster x Drosophila simulans

Type:

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

Platforms:

GPL34386 GPL25244 GPL33169

12 Samples

Download data

(Submitter supplied) Species of the genus Drosophila have served as favorite models in speciation studies, however genetic factors of the interspecific hybrid sterility are underinvestigated to date. Here we performed the analysis of reproductive incompatibilities of hybrid females in crossing Drosophila melanogaster females and Drosophila simulans males. Using transcriptomic data analysis, molecular, cellular and genetic approaches we analyzed differential gene expression, transposable element (TE) activity, piRNA biogenesis and functional defects of oogenesis in hybrids. more...

Organism:

Drosophila simulans; Drosophila melanogaster; Drosophila melanogaster x Drosophila simulans

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL25244 GPL33169 GPL34386

6 Samples

Download data: CSV

(Submitter supplied) Species of the genus Drosophila have served as favorite models in speciation studies, however genetic factors of the interspecific hybrid sterility are underinvestigated to date. Here we performed the analysis of reproductive incompatibilities of hybrid females in crossing Drosophila melanogaster females and Drosophila simulans males. Using transcriptomic data analysis, molecular, cellular and genetic approaches we analyzed differential gene expression, transposable element (TE) activity, piRNA biogenesis and functional defects of oogenesis in hybrids. more...

Organism:

Drosophila simulans; Drosophila melanogaster; Drosophila melanogaster x Drosophila simulans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33169 GPL25244 GPL34386

6 Samples

Download data: CSV

(Submitter supplied) Genome organization can regulate gene expression and promote cell fate transitions. The differentiation of germline stem cells (GSCs) to oocytes in Drosophila involves changes in genome organization mediated by heterochromatin and the nuclear pore complex (NPC). Heterochromatin represses germ-cell genes during differentiation and NPCs anchor these silenced genes to the nuclear periphery, maintaining silencing to allow for oocyte development. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

5 Samples

Download data: CSV

(Submitter supplied) The objective of the study was to examine the gene expression changes caused by human DNMT3L overexpression in Drosophila melanogaster brains. There were 6 samples in total- C1, C2, C3, D1, D2, and D3. C1-C3 were larvae brains from the strain of elavC155-Gal4, which were used as the control group (C). D1-D3 were larvae brains from the strain with DNMT3L overexpression, which were bred by crossing the strains of elavC155-Gal4 and w/w;P(UAS-DNMT3L,w+)/Cyo;TM2/TM6B and used as the DNMT3L overexpressing group (D). more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23323

6 Samples

Download data: TXT

(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

Platforms:

GPL25244 GPL19132

37 Samples

Download data: BED, BW

(Submitter supplied) Genome organization can regulate gene expression and promote cell fate transitions. The differentiation of germline stem cells (GSCs) to oocytes in Drosophila involves changes in Genome organization mediated by heterochromatin and the nuclear pore complex (NPC). Heterochromatin represses germ-cell genes during differentiation and NPCs anchor these silenced genes to the nuclear periphery, maintaining silencing to allow for oocyte development. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25244

24 Samples

Download data: BED, BW