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Items: 1 to 20 of 1782

1.

Hormetic response and transcriptome profiling reveal the mechanism underlying metabolic and cuticular resistance to host-specific terpenoid defenses in an emerging insect pest, Pagiophloeus tsushimanus (coleoptera: curculionidae)

(Submitter supplied) The resistance mechanisms evolved by insects to overcome host-plant allelochemicals is a key consideration in pest management. Camphor oil (EO) and its main component (i.e D-camphor) form a specific terpenoid-defensive system in camphor trees, Cinnamomum camphora. However, an emerging insect pest, Pagiophloeus tsushimanus has recently caused serious damage to this intractable plant species, which is largely elusive. more...
Organism:
Pagiophloeus tsushimanus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30528
15 Samples
Download data: FASTA, TXT
Series
Accession:
GSE182420
ID:
200182420
2.

Host-specific gene expression as a tool for introduction success in Naupactus parthenogenetic weevils

(Submitter supplied) Food resource access can mediate establishment success in invasive species, and generalist herbivorous insects are thought to rely on mechanisms of transcriptional plasticity to respond to dietary variation. While asexually reproducing invasives typically have low genetic variation, the twofold reproductive capacity of asexual organisms is a marked advantage for colonization. We studied host-related transcriptional acclimation in parthenogenetic, invasive, and polyphagous weevils: Naupactus cervinus and N. more...
Organism:
Naupactus cervinus; Naupactus leucoloma
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL30096 GPL30090
52 Samples
Download data: CSV, FASTA
Series
Accession:
GSE173980
ID:
200173980
3.

Application of a classifier combining bronchial genomics and chest CT features facilitates the diagnostic evaluation of lung cancer in smokers and non-smokers

(Submitter supplied) Introduction: Lung cancer screening by computed tomography (CT) reduces mortality but exhibited high false-positive rates. We established a diagnostic classifier combining chest CT features with bronchial genomics. Materials and Methods: Patients with CT-detected suspected lung cancer were enrolled. The sample collected by bronchial brushing was used for RNA sequencing. R software was applied to build the model. more...
Organism:
Bronchus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29733
283 Samples
Download data: TXT
Series
Accession:
GSE166926
ID:
200166926
4.

Expression analysis of genes related to cold tolerance in Dendroctonus valens

(Submitter supplied) To identify genes relevant to cold tolerance and the process of overwintering, we sequenced the transcriptomes of wintering and non-wintering adult and larval D. valens using the Illumina HiSeq platform. Differential expression analysis methods for other non-model organisms were used to compare transcript abundances in adults and larvae at two time periods, followed by the identification of functions and metabolic pathways related to genes associated with cold tolerance. more...
Organism:
Dendroctonus valens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29012
12 Samples
Download data: FASTA, TXT
Series
Accession:
GSE156139
ID:
200156139
5.

Genomic structural and transcriptional variation of Oryctes rhinoceros nudivirus (OrNV) in Coconut Rhinoceros Beetle 

(Submitter supplied) Oryctes rhinoceros nudivirus (OrNV) is a dsDNA virus which has been used as a biocontrol agent to suppress Coconut Rhinoceros Beetle (Oryctes rhinoceros) in Southeast Asia and the Pacific Islands. Recently a new wave of O. rhinoceros incursions in Oceania is thought to be related to the presence of low virulence isolates of OrNV or virus tolerant haplotypes of beetles. Here, chronically infected beetles were collected from the Philippines, Fiji, PNG and the Solomon Islands (SI). more...
Organism:
Oryctes rhinoceros
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL28699
11 Samples
Download data: XLSX
6.

Transcriptome of Tribolium castaneum selection lines (control-, drought-, heat-, heat/drought-adapted) under different climatic conditions

(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
Series
Accession:
GSE156256
ID:
200156256
7.

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

(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
Series
Accession:
GSE155634
ID:
200155634
8.

Beetle horns evolved from wing serial homologs

(Submitter supplied) Understanding how novel complex traits originate is a foundational challenge in evolutionary biology. Yet how descent with modification in developmental evolution may lead to morphological innovation remains poorly understood. We investigated the origin of thoracic horns in scarabaeine beetles, one of the most dramatic classes of secondary sexual traits in the animal kingdom. We show that thoracic horns derive from bilateral source tissues, that diverse wing genes are functionally required for instructing this process, and that in the absence of Hox-input thoracic horn primordia transform to contribute to ectopic wings. more...
Organism:
Onthophagus taurus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL22541
60 Samples
Download data: TSV
Series
Accession:
GSE137455
ID:
200137455
9.

Exploring the integration of innovation in the dorsal head of Onthophagus beetles using head compartment-specific RNAseq

(Submitter supplied) The general morphology of the insect head has remained relatively unchanged through more than 400 million years of evolution. Yet throughout this period this same region has also become a hotspot for evolutionary novelty, yielding structures such as the eyestalks of stalk-eyed flies or the cephalic horns of dung beetles. How novelty can be integrated within ancient complex traits without disrupting the function and formation of that trait is a foundational, yet largely unresolved question in developmental and evolutionary biology. more...
Organism:
Onthophagus taurus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL22541
66 Samples
Download data: TSV
Series
Accession:
GSE136677
ID:
200136677
10.

Tribolium castaneum experimental evolution

(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
Series
Accession:
GSE133892
ID:
200133892
11.

Transcriptome of Tribolium castaneum in different climatic conditions

(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
Series
Accession:
GSE133570
ID:
200133570
12.

Differentially and co-expressed genes in embryo, germ-line and somatic tissues of Tribolium castaneum

(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
Series
Accession:
GSE119739
ID:
200119739
13.

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

(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
Series
Accession:
GSE120735
ID:
200120735
14.

Application of Chromatrap® Solid-State Chromatin Immunoprecipitation (ChIP) for epigenetic profiling of insects

(Submitter supplied) We report the application of Chromatraps® Solid-State Chromatin Immunoprecipitation technology for epigenetic profiling of histone modifications in insects. Here, we present the optimised protocol and conditions of Chromatrap® kits for successful ChIP and high-throughput sequencing of established model species, Drosophila melanogaster and the emerging model for behavioural plasticity Nicrophorus vespilloides. more...
Organism:
Nicrophorus vespilloides; Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL16479 GPL25731
16 Samples
Download data: BED
Series
Accession:
GSE121855
ID:
200121855
15.

Next Generation Sequencing to determine the fundamental mechanisms of Tribolium castaneum larvae to cope with hypoxia

(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
Series
Accession:
GSE114049
ID:
200114049
16.

Firefly genomes illuminate parallel origins of bioluminescence in beetles

(Submitter supplied) Fireflies and their fascinating luminous courtships have inspired centuries of scientific study. Today firefly luciferase is widely used in biotechnology, but the evolutionary origin of their bioluminescence remains unclear. To shed light on this long-standing question, we sequenced the genomes of two firefly species that diverged over 100 million-years-ago: the North American Photinus pyralis and Japanese Aquatica lateralis. more...
Organism:
Photinus pyralis
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL24293
4 Samples
Download data: TSV
Series
Accession:
GSE107177
ID:
200107177
17.

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

(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
Series
Accession:
GSE104495
ID:
200104495
18.

miRNA expression in Anopheles gambiae tissues

(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:
Bombyx mori; Drosophila melanogaster; Tribolium castaneum; Aedes aegypti; Anopheles gambiae; Culex quinquefasciatus; Apis mellifera
Type:
Non-coding RNA profiling by array
Platform:
GPL23950
40 Samples
Download data: TXT
Series
Accession:
GSE103034
ID:
200103034
19.

Therapeutic antibodies to ganglioside GD2 evolved from highly selective germline antibodies

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Gossypium hirsutum; Pandalus borealis; Oncorhynchus nerka; Homo sapiens; Sus scrofa domesticus; Gallus gallus; Oryctolagus cuniculus; Mus musculus; Human immunodeficiency virus 1; unidentified; Megathura crenulata; Rhodotorula; Bos taurus; Ovis aries; Ceratonia siliqua; Frangula alnus; Senegalia senegal; Dermestes lardarius; Quercus alba; Trypanosoma cruzi; Bothrops moojeni; Pachymenia carnosa
Type:
Protein profiling by protein array
Platforms:
GPL23565 GPL23566
55 Samples
Download data: GPR
Series
Accession:
GSE100438
ID:
200100438
20.

Therapeutic antibodies to ganglioside GD2 evolved from highly selective germline antibodies VII

(Submitter supplied) Purpose: This study uses a high-throughput glycan microarray to evaluate the immunological evolution of antibodies to the glyco-antigen GD2. The goal is to determine germline and affinity mature antibody specificity and affinities/ Results: Affinity mature anti-GD2 antibodies 3F8 and ch14.18 had high affinity and were highly specific for the target GD2. Germline antibodies were also hihgly specific and had surprisingly high affinity. more...
Organism:
Ovis aries; Oryctolagus cuniculus; Megathura crenulata; Frangula alnus; Quercus alba; Pandalus borealis; Oncorhynchus nerka; Sus scrofa domesticus; Ceratonia siliqua; Bothrops moojeni; Senegalia senegal; Dermestes lardarius; Trypanosoma cruzi; Gallus gallus; Pachymenia carnosa; Gossypium hirsutum; Rhodotorula; Homo sapiens; Bos taurus; Mus musculus; Human immunodeficiency virus 1
Type:
Protein profiling by protein array
Platform:
GPL23566
7 Samples
Download data: GPR, TXT
Series
Accession:
GSE100310
ID:
200100310
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