Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Survey of methylomes of two beetles, Nicrophorus vespilloides and Tribolium castaneum

ABSTRACT: 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(S): Tribolium castaneum Nicrophorus vespilloides

PROVIDER: GSE68814 | GEO | 2015/10/21

SECONDARY ACCESSION(S): PRJNA283826

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Deep sequencing of small RNAs from Tribolium castaneum

Project description:Characterization of miRNAs in red flour beetle Tribolium castaneum by deep sequencing of two different RNA libraries. Sequencing of Tribolium small RNAs from adults and embryos.

2010-12-29 | E-GEOD-26036 | biostudies-arrayexpress

Deep sequencing of small RNAs from Tribolium castaneum

Project description:Characterization of miRNAs in red flour beetle Tribolium castaneum by deep sequencing of two different RNA libraries.

2010-12-29 | GSE26036 | GEO

Genome-wide survey of transcriptional differences between males and females of Tribolium castaneum, the red flour beetle

Project description:Genome-wide survey of transcriptional differences between males and females of Tribolium castaneum, the red flour beetle Four biological replicates for male and female beetles with 20 individuals per replicate. Two technical replicates, one replicate per sex. 16,434 genes/expressed non-coding regions represented twice on each array. Three 60 mer probes for most exons/expressed non-coding regions. 167,538 unique genomic probes replicated twice per array.

2010-05-26 | E-GEOD-18087 | biostudies-arrayexpress

Genome-wide survey of transcriptional differences between males and females of Tribolium castaneum, the red flour beetle

Project description:Genome-wide survey of transcriptional differences between males and females of Tribolium castaneum, the red flour beetle

2010-05-27 | GSE18087 | GEO

Dnmt1 has an essential function despite the absence of CpG DNA methylation in the red flour beetle Tribolium castaneum

Project description: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. The red flour beetle, Tribolium castaneum, lacks Dnmt3 but possesses Dnmt1 and it has been controversial whether it has a functional DNA methylation system. Using whole genome bisulfite sequencing, we did not find any defined patterns of CpG DNA methylation in embryos. Nevertheless, we found Dnmt1 expressed throughout the entire life cycle of the beetle, with mRNA transcripts significantly more abundant in eggs and ovaries. A maternal knockdown of Dnmt1 caused a developmental arrest in offspring embryos. We show that Dnmt1 plays an essential role in T. castaneum embryos and that its downregulation leads to an early developmental arrest. This function appears to be unrelated to DNA methylation, since we did not find any evidence for this modification. This strongly suggests an alternative role of this protein.

2018-11-14 | GSE120735 | GEO

Metabolic and transcriptome responses of RNAi-mediated AMPKα knockdown in Tribolium castaneum

Project description: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. Results: RNAi-mediated suppression of TcAMPKα increased whole-body triglyceride (TG) level and the ratio between glucose and trehalose, as was confirmed by in vivo treatment with the AMPK-activating compound, 5-Aminoimidazole-4-carboxamide1-β-D-ribofuranoside (AICAR). A total of 1184 differentially expressed genes (DEGs) were identified between dsTcAMPKα-injected and dsEGFP-injected beetles. These include genes involved in lipid and carbohydrate metabolism as well as insulin/insulin-like growth factor signaling (IIS). Real-time quantitative polymerase chain reaction analysis confirmed the differential expression of selected genes. Interestingly, metabolism-related transcription factors such as sterol regulatory element-binding protein 1 (SREBP1) and carbohydrate response element-binding protein (ChREBP) were also significantly upregulated in dsTcAMPKα-injected beetles. Conclusions: AMPK plays a critical role in the regulation of beetle metabolism. The findings of DEGs involved in lipid and carbohydrate metabolism provide valuable insight into the role of AMPK signaling in the transcriptional regulation of insect metabolism.

2020-08-04 | GSE155634 | GEO

Enhancer identification and activity evaluation in the red flour beetle, Tribolium castaneum

Project description: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. Comparison of these profiles revealed a distinct set of open chromatin regions in each tissue and stage. Second, we established the first reporter assay system that works in both Drosophila and Tribolium, using nubbin in the wing and hunchback in the embryo as case studies. Together, these advances will be useful to study the evolution of cis-language and morphological diversity in Tribolium and other insects.

2017-10-03 | GSE104495 | GEO

Tribolium castaneum

Project description:Tribolium castaneum phosphine

| PRJNA297896 | ENA

Tribolium castaneum

Project description:Tribolium castaneum Proteome

| PRJNA257028 | ENA

Identification of maternally-loaded RNA transcripts in unfertilized eggs of Tribolium castaneum

Project description:Using a tiled whole-genome microarray, we found that 58.2% of Tribolium castaneum genes are maternally loaded into eggs. Comparison of known Drosophila melanogaster maternal genes to our results showed widespread conservation of maternal function with T. castaneum. We also found many T. castaneum genes with previously identified gender or tissue specific expression were also maternally loaded into eggs. The microarray design also allowed the detection of 2315 and 4060 novel transcriptionally active regions greater in length than 100 bp in unfertilized and fertilized T. castaneum eggs, respectively. The primary objective of this study was to identify expressed regions of the Tribolium castaneum genome in unfertilized and fertilized eggs using a whole-genome tiled microarray. The whole RNA of 3 samples of virgin laid eggs and 3 samples of fertilized eggs were compaired.

2013-05-06 | E-GEOD-38245 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data