GEO DataSets

(Submitter supplied) A key problem in development is to understand how genes turn on or off at the right place and right time during embryogenesis. Such decisions are made by non-coding sequences called 'enhancers.' Much of our models of how enhancers work rely on the assumption that genes are activated de novo as stable domains across embryonic tissues. Such a view has been strengthened by the intensive landmark studies of the early patterning of the anterior-posterior (AP) axis of the Drosophila embryo, where indeed gene expression domains seem to arise more or less stably. more...

Organism:

Tribolium castaneum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL33513

18 Samples

Download data: BW

(Submitter supplied) We investigate tissue transcriptomic evolution across bilaterian animals by analyzing RNA-seq data from eight different tissues across twenty species.

Organism:

Tribolium castaneum; Aedes aegypti; Xenopus tropicalis; Cloeon dipterum; Bombyx mori; Drosophila melanogaster; Callorhinchus milii; Monodelphis domestica; Episyrphus balteatus; Branchiostoma lanceolatum; Danio rerio; Blattella germanica; Strongylocentrotus purpuratus; Octopus bimaculoides; Strigamia maritima

Type:

Expression profiling by high throughput sequencing

15 related Platforms

89 Samples

Download data: TSV

(Submitter supplied) We studied plastic and evolutionary responses in gene expression of Tribolium castaneum after beetles’ exposure to new environments that differed from ancestral control conditions in temperature, humidity or both. Using experimental evolution with ten replicated lines per condition, we were able to demonstrate adaptation (higher offspring number compared to control lines) after 20 generations. We measured whole-transcriptome gene expression with RNA-seq to infer evolutionary and plastic changes. more...

Organism:

Tribolium castaneum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20193

244 Samples

Download data: TXT

(Submitter supplied) Background: The AMP-activated protein kinase (AMPK) is an intracellular fuel sensor for lipid and glucose metabolism. In addition to the short-term regulation of metabolic enzymes by phosphorylation, AMPK may also exert long-term effects on the transcription of downstream genes through the regulation of transcription factors and coactivators. In this study, RNA interference (RNAi) was conducted to investigate the effects of knockdown of TcAMPKα on lipid and carbohydrate metabolism in the red flour beetle, Tribolium castaneum, and the transcriptome profiles of dsTcAMPKα-injected and dsEGFP-injected beetles under normal conditions were compared by RNA-sequencing. more...

Organism:

Tribolium castaneum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18162

6 Samples

Download data: TXT

(Submitter supplied) We report Illumina-generated RNASeq data of several populations of Tribolium castaneum larvae selected for higher or lower immune priming specificity as well as unselected control populations. From each of these populations, we injected groups of 20 larvae with either one of three bacteria species or left them untreated as controls. Whole body samples were taken 6h after injection and used for RNASeq Analysis.

Organism:

Tribolium castaneum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18162

60 Samples

Download data: TXT

(Submitter supplied) We combined fitness and whole-transcriptome data of Tribolium castaneum to investigate gene expression and fitness responses to drought, heat and their combination. Fitness was reduced by both stressors and their combined effects were nearly additive. Accordingly, expression data showed that both stressors were acting mostly independently and did not interfere physiologically. Response to heat stress resulted in a much higher number of differentially expressed genes compared to drought stress. more...

Organism:

Tribolium castaneum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20193

183 Samples

Download data: TXT

(Submitter supplied) Transcriptomic studies of Tribolium castaneum have led to significant advances in our understanding of co-regulation and differential expression of genes in development. However, previously used microarray approaches have covered only a subset of known genes. The aim of this study was to investigate gene expression patterns of beetle embryo, germ-line and somatic tissues. We identified 12,302 expressed genes and determined differentially expressed up and down-regulated genes among all samples. more...

Organism:

Tribolium castaneum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20193

17 Samples

Download data: CSV, TAR

(Submitter supplied) Epigenetic mechanisms, such as CpG DNA methylation enable phenotypic plasticity and rapid adaptation to changing environments. CpG DNA methylation is established by DNA methyltransferases (DNMTs), which are well conserved across vertebrates and invertebrates. There are insects with functional DNA methylation despite lacking a complete set of Dnmts. But at least one of the enzymes, DNMT1, appears to be required to maintain an active DNA methylation system. more...

Organism:

Tribolium castaneum

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL18255

2 Samples

Download data: TXT

(Submitter supplied) We used high-throughput sequencing technology to determine the fundamental mechanisms of Tribolium castaneum to cope with hypoxia. Totals of 12,524,554 useful reads from the control group and 14,193,339 useful reads from the treatment group were generated after Q20 filtering. A total of 16,524 unigenes had been annotated. More than 300 transcripts showed differential expression between the control and hypoxia group, with a fold change ≥1.5 and p value <0.05. more...

Organism:

Tribolium castaneum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20193

2 Samples

Download data: GTF

(Submitter supplied) Evolution of cis-properties (such as enhancers) often plays an important role in the production of diverse morphology. However, a mechanistic understanding is often limited by the absence of methods to study enhancers in species outside of established model systems. Here, we sought to establish methods to identify and test enhancer activity in the red flour beetle, Tribolium castaneum. To identify possible enhancer regions, we first obtained genome-wide chromatin profiles from various tissues and stages of Tribolium via FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)-sequencing. more...

Organism:

Tribolium castaneum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18255

16 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Anopheles gambiae mosquitoes transmit the human malaria parasite Plasmodium falciparum, which causes the majority of fatal malaria cases worldwide. The hematophagous life style defines the mosquito reproductive biology and is exploited by P. falciparum for its own sexual reproduction and transmission. The two main phases of the mosquito reproductive cycle, pre-vitellogenic (PV) and post-blood meal (PBM) shape its capacity to transmit malaria. more...

Organism:

Tribolium castaneum; Aedes aegypti; Anopheles gambiae; Culex quinquefasciatus; Apis mellifera; Bombyx mori; Drosophila melanogaster

Type:

Non-coding RNA profiling by array

Platform:

GPL23950

40 Samples

Download data: TXT

(Submitter supplied) Cytosine DNA methylation in the Tribolium castaneum has been controversial, its distribution pattern and functions have not been established yet. Here, using BS-Seq, we confirmed the existence of DNA methylation and described the methylation profiles for four life stages of T.castaneum. Interestingly, two types of DNA methylation had been discovered in T.castaneum genome. One was the symmetrical CpG methylation which was typically existed among eukaryotes methylomes, but occupied small part in methylome of T. more...

Organism:

Tribolium castaneum

Type:

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

Platform:

GPL22138

8 Samples

Download data: TAR, TXT

(Submitter supplied) We report the temporal dynamics of differential gene expression between primed and unprimed beetles infected with the entomopathogen Bt

Organism:

Tribolium castaneum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18255

48 Samples

Download data: TXT

(Submitter supplied) To identify miRNAs of Tribolium castaneum, one small RNA libraries for mix samples of eight development stage (including 1-day-old early embryo, 3-day-old late embryo, 1-day-old early larva, 20-day-old late larva, 1-day-old early pupa, 6-day-old late pupa, 1-day-old early adult, 7-day-old late adult) were constructed. Totally, 12,259,974 raw reads were obtained, 7,116,806 mappable reads were remained and 2,175,311 high-quality miRNA reads were identified after the small RNA digitalisation analysis. more...

Organism:

Tribolium castaneum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9920

1 Sample

Download data: XLSX

(Submitter supplied) This study examines gene expression differences between infected larvae from different maternal infection backgrounds to try to understand the immunological basis of invertebrate immune priming. Female Tribolium castaneum beetles were either jabbed with sterile saline, heat killed Bt, or left naïve. 15 Offspring from the first and second broods were infected with Bt and 24 hours later pooled by treatment and flash frozen Beetles from saline and primed maternal backgrounds are compared to naïve infected

Organism:

Tribolium castaneum

Type:

Expression profiling by array

Platform:

GPL16756

2 Samples

Download data: TXT

(Submitter supplied) The presence of DNA methylation in beetles (Coleoptera) has only been investigated with bisulfite sequencing of Tribolium castaneum, which produced no evidence of DNA methylation. Here, we used whole genome bisulfite sequencing to assay if DNA methylation was present in another beetle, Nicrophorus vespilloides. We used T. castaneum as a negative control.

Organism:

Nicrophorus vespilloides; Tribolium castaneum

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL20192 GPL20193

6 Samples

Download data: TSV, TXT

(Submitter supplied) Next generation sequencing analysis of the small RNA and RNA profiles of successive time intervals during T. castaneum embryogenesis, and Drosophila unfertilized oocytes

Organism:

Drosophila melanogaster; Tribolium castaneum; Drosophila virilis

Type:

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

4 related Platforms

22 Samples

Download data: TXT

(Submitter supplied) Chemoreception is based on the senses of smell and taste that are crucial for animals to find new food sources, shelter, and mates. The initial step in olfaction involves the translocation of odorants from the periphery through the aqueous lymph of the olfactory sensilla to the odorant receptors by chemosensory proteins (CSPs) or odorant binding proteins (OBPs).To better understand the roles of CSPs and OBPs in a coleopteran pest species, the red flour beetle Tribolium castaneum (Coleoptera, Tenebrionidae), we performed transcriptome analyses of male and female antennae, heads, mouthparts, legs, and bodies, which revealed that all 20 CSPs and 49 of the 50 previously annotated OBPs are transcribed. more...

Organism:

Tribolium castaneum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18255

16 Samples

Download data: FA, TXT

(Submitter supplied) Drosophila larvae and adults possess a potent innate immune response, but the response of their eggs is particularly poor. Here we show that eggs of the beetle Tribolium castaneum, in contrast, possess a full range of immune defence mechanisms, based on complete transcriptome comparisons of naïve, sterilely injured, and bacterially challenged eggs. Upon infection, we find massive upregulation of AMPs and differential regulation of 375 other genes including both IMD and Toll signalling components. more...

Organism:

Tribolium castaneum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18162

27 Samples

Download data: TXT

(Submitter supplied) Purpose: Combination of systemic RNAi with RNAseq to identify target genes of important pathways in early development Wnt/β-catenin and hedgehog (Hh) signaling are essential for transmitting signals across cell membranes in animal embryos. Early patterning of the principal insect model, Drosophila melanogaster, occurs in the syncytial blastoderm, where diffusion of transcription factors obviates the need for signaling pathways. more...

Organism:

Tribolium castaneum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18255

25 Samples

Download data: TXT