Genome-wide transcriptional analysis of PTTH-stimulated Bombyx prothoracic gland
Ontology highlight
ABSTRACT:
ORGANISM(S): Bombyx mori
SUBMITTER: Kirst King-Jones
PROVIDER: E-GEOD-84963 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:To identify the cuticular proteins in developing wing scales of Bombyx mori, we performed LC-MS/MS analysis of dissoliving developing wing scales from Bombyx mori
2021-04-26 | PXD024341 | Pride
Project description:To identify the cuticular proteins in developing wing scales of Bombyx mori, we performed LC-MS/MS analysis of dissoliving developing wing scales from Bombyx mori
2021-04-26 | PXD024362 | Pride
Project description:To identify the cuticular proteins in developing wing scales of Bombyx mori, we performed LC-MS/MS analysis of dissoliving developing wing scales from Bombyx mori
2021-04-26 | PXD024365 | Pride
Project description:Amongst the various different insect groups, there is remarkable diversity in the number and size of wings. However the development of the basic body plan in insects is similar to a large extent. The genes of the hox complex regulate various pathways to bring about the development or modification of different organs. Ubx, a gene of the bithorax hox complex is expressed in the third thoracic segment of insects and is known to specify the fate of wing appendage in that segment.To understand the role of Ubx and how its regulatory mechanism has evolved through the course of evolution we have compared its genome wide targets in different insect orders. The identification of regulatory pathways and the key players Ubx regulates is crucial to understand how it has controlled wing development across insect orders. Our lab has previously identified direct targets of Ubx in Drosophila using ChIP-chip (Agrawal et al, 2011). To further our knowledge on the role of regulation in development and modification of hind wing appendage we have studied the targets in the hind wings of other insects (silk moth; Lepidoptera and honeybee; Hymenoptera) and performed a comparative analysis. We have employed ChIP followed by illumina sequencing to identify the targets of Ubx in developing hind and fore wing buds of Bombyx larvae. This is a first next generation sequencing study in Lepidoptera in an attempt to understand wing development. Chromatin Immunoprecipitation (ChIP) was used to identify genome wide targets bound by Ubx in Bombyx larval wing buds. The experiment to enrich Ubx bound regions was carried out using a Bombyx N terminal-Ubx specific poylclonal antibody raised in Rabbit and purified against a Protein A column to obtain IgG fraction. An Immunoprecipitation (IP) with Normal Rabbit IgG was used as a negative control to eliminate the regions that pertained to non specific binding to an Immunogloubulin. The normalization of both ChIP and IgG was done against sequenced input chromatin. Two replicates of single end 36 bp reads were sequenced using Ilumina for all the three conditions and for both fore and hind wing tissue samples.The peaks common to both the replicates were considered after applying a FDR cutoff.The fore wing target set was used for comparison with the hind wing targets.
2016-07-27 | E-GEOD-71990 | biostudies-arrayexpress
Project description:Amongst the various different insect groups, there is remarkable diversity in the number and size of wings. However the development of the basic body plan in insects is similar to a large extent. The genes of the hox complex regulate various pathways to bring about the development or modification of different organs. Ubx, a gene of the bithorax hox complex is expressed in the third thoracic segment of insects and is known to specify the fate of wing appendage in that segment.To understand the role of Ubx and how its regulatory mechanism has evolved through the course of evolution we have compared its genome wide targets in different insect orders. The identification of regulatory pathways and the key players Ubx regulates is crucial to understand how it has controlled wing development across insect orders. Our lab has previously identified direct targets of Ubx in Drosophila using ChIP-chip (Agrawal et al, 2011). To further our knowledge on the role of regulation in development and modification of hind wing appendage we have studied the targets in the hind wings of other insects (silk moth; Lepidoptera and honeybee; Hymenoptera) and performed a comparative analysis.To understand the differential development of wing appendages in insects we intend to compare the differential expression of fore and hind wing appendages in Diptera and Lepidoptera. We have employed RNA-seq using by illumina sequencing to identify the genes that are differentially expressed between fore and the hind wing bud of the Bombyx larvae. Only one replicate was performed as the intended study was to validate the differential targets in comparison to ChIP studies and other methods of select candidates. Total RNA was extarcted from wing buds of IV instar Bombyx larvae and sequenced on an illumina sequencer. Wing buds were collected directly in liquid nitrogen and 80 such buds each for fore and hind wing were collected from IV instar larvae. RNA was isolated from them and processed for Library preperation and illumina sequencing. One replicate was done as a supplement to ChIP studies.
2016-07-27 | E-GEOD-71988 | biostudies-arrayexpress
Project description:This is part of a cross-species approach to characterize transcriptional response of the insect prothoracic gland (PG) to the prothoracicotropic hormone (PTTH). Genome-wide response of the PG to PTTH was analyzed in vitro in Bombyx and in vivo in Drosophila, and the results were compared to identify common components in the PTTH signaling pathway.
2016-07-29 | GSE84963 | GEO
Project description:As important roles of small RNA pathways, AGO proteins mediate interaction of incorporated small RNAs with their targets. The resolution of AGO associated small RNAs showed a significant landscape of AGO proteins and their binding small RNAs. To characterize small RNAs that associated with BmAGO2 protein in Bombyx mori, the small RNA population associated with BmAGO2 in BmN cells was extracted from the AGO immunoprecipitated complex and the small RNAs between 17nt to 50nt separated by a polyacrylamide gel electrophoresis were subjected to library construction and deep sequencing.The high throughput sequencing yielded a total of 11691441 reads, representing 813,702 unique reads with a abundance from 5731905 to 1. Small RNA associated with AGO2 of BmN cell infected with ie1-bacmid recombinant viruses were performed by high-throughput using Hiseq 2000.
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Project description:MicroRNAs (miRNAs) as small non-coding RNAs play important roles in many biological processes such as development, cell signalling and immune response. Studies also suggest that miRNAs are important in host–virus interactions where the host limits virus infection by differentially expressing miRNAs that target essential viral genes. Here, we identified conserved and new miRNAs from Spodoptera frugiperda cells (Sf9) using a combination of deep sequencing and bioinformatics as well as experimental approaches. S. frugiperda miRNAs share common features of miRNAs in other organisms, such as uracil (U) at the 59 end of miRNA. The 59 ends of the miRNAs were more conserved than the 39 ends, revealing evolutionary protection of the seed region in miRNAs. The predominant miRNAs were found to be conserved among arthropods. The majority of homologous miRNAs were found in Bombyx mori, with 76 of the 90 identified miRNAs. We found that seed shifting and arm switching have happened in this insect’s miRNAs. Expression levels of the majority of miRNAs changed following baculovirus infection. Results revealed that baculovirus infection mainly led to an overall suppression of cellular miRNAs. We found four different genes being regulated by sfr-miR-184 at the post-transcriptional level. The data presented here further support conservation of miRNAs in insects and other organisms. In addition, the results reveal a differential expression of host miRNAs upon baculovirus infection, suggesting their potential roles in host–virus interactions. Seed shifting and arm switching happened during evolution of miRNAs in different insects and caused miRNA diversification, which led to changes in the target repository of miRNAs. Identification of miRNA and other small non coding RNA in NPV infected Sf9 cells
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Project description:Bufotoxin is an endogenous toxin made up of several physiologically active components that toads deploy as a defense against their natural enemies. Bufadienolides (BDS), which is isolated from bufotoxin, is an important anticancer drug, and other components such as bufotenine and alkaloids are also important drug resources. The distribution characteristics and biosynthesis of bufotoxins in the postauricular glands (PGs) of toads are not well understood. We examined the toad's PGs using the MADLI/MSI technique, a total of 1,872 components were found, and some pharmacological components were visible. These findings indicate that bufotoxins are primarily abundant in the plasma glands (pG) and epidermal tissues of the glands. By using single-cell sequencing, it was possible to create a single-cell atlas of 9316 PGs cells. These cells were then categorized into nine clusters using marker genes, and two types of epithelial cells were verified using in situ hybridization investigations. It was confirmed that cholesterol is a precursor component of BDS biosynthesis, we concentrated on the cholesterol metabolism component and postulated the primary bile acid pathway as a downstream biosynthesis pathway of BDS through transcriptomic studies of two pG and mucous glands (MG) with distinct secretory functions. Optimal and silenced genes for potential BDS synthesis pathways, toad toxin tryptamine and alkaloid biosynthesis, terpene skeleton and steroid hormones were identified by calculating the cellular coverage of genes. Our data demonstrate the metabolic mapping of bufotoxins in the PGs of the toad, and create the first single-cell atlas of PGs in the toad, providing a reference for the study of biosynthesis of natural active ingredients in animals.
2024-11-05 | PXD057113 | Pride
Project description:The project aim was to identify the cell membrane receptors that prothoracic gland cells use to decode and transduce information from the extracellular environment during the final larval stage of the model insect, Bombyx mori.
2016-01-27 | PXD002771 | Pride