Differentially expressed genes (DEGs) in oviducts of Yun7 and its giant egg mutant Yun7Ge of silkworm, Bombyx mori
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA726569 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14371759_1.fastq.gz | Fastqsanger.gz | |||
| SRR14371759_2.fastq.gz | Fastqsanger.gz | |||
| SRR14371760_1.fastq.gz | Fastqsanger.gz | |||
| SRR14371760_2.fastq.gz | Fastqsanger.gz | |||
| SRR14371761_1.fastq.gz | Fastqsanger.gz |
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Project description:Changes in gene expressions associated with egg diapause in multivoltine silkworm Bombyx mori
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Project description:Changes in gene expressions associated with egg diapause in multivoltine silkworm Bombyx mori Agilent one-color experiment, Agilent-Custom : Bombyx mori 4x44k designed by Genotypic Technology Pvt. Ltd. (AMADID: 034793) , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0444)
2012-09-30 | E-GEOD-35622 | biostudies-arrayexpress
Project description:Yun7Ge (Yun7Ge is represented by Ge in the high-throughput sequencing results) is a giant egg mutant found in the silkworm variety Yun7 (Yun7 is represented by Se in the high-throughput sequencing results). The amount of laid eggs and the hatching rate of Yun7Ge are reduced, which is not conducive to the reproduction. The target gene controlling giant egg trait is located on the Z chromosome (chromosome 1) was determined through genetic analysis. To find mutant gene and explore the relationship between mutant gene and giant egg trait, the differentially expressed genes (DEGs) in the oviducts of Yun7 and Yun7Ge were analyzed by high-throughput sequencing, and two replicates were set for each sample. ∣log 2∣>1, the value of FPKM>100 and the genes were up-regulated or down-regulated in giant eggs of the two replicates as the standard for screening DEGs. A total of 65 DEGs were screened. Among these DEGs, 7 genes were up-regulated and 58 genes were down-regulated in giant eggs. These DEGs were classified according to the chromosome where the genes are located. The results showed that there was only one DEG (PHYHD1) on chromosome Z, and it was almost not expressed in giant eggs. Interestingly, there were 35 DEGs on chromosome 2, including 25 chorion genes, and these 25 genes are all down-regulated. After knocking out the PHYHD1 using CRISPR/Cas9, the chorion genes were significantly down-regulated. These results indicate that the silencing of PHYHD1 leads to the down-regulation of many chorion protein genes, which may be the direct cause of giant eggs.
2021-05-01 | GSE173672 | GEO
Project description:The silkworm, Bombyx mori, is a complete metamorphosis insect and an economically important for silk production, the model to study insect physiology and biochemistry. Bombyx mori nucleopolyhedrovirus (BmNPV) is a principal pathogen of the silkworm and its host range is restricted to silkworm larvae, requiring interaction with silkworm larvae to accomplish virus replication. Prothoracic glands (PGs) are a model for synthetic ecdysone with regulating insect growth and development. In this study, day-4 fifth instar silkworm larvae were infected by BmNPV, the wandering silkworms appeared in the infected groups were 12 hours earlier than that in the control groups, and the ecdysone titer in infected larvae was significantly higher than that of the control larvae. Then, we used RNA sequencing (RNA-seq) to analyze silkworm PGs 48 h after BmNPV infection. The classifications of the 15 differential expression genes (DEGs) were mainly involved in the metabolic processes and pathways. The RT-qPCR results of the DEGs in the PGs of BmNPV-infected at 24, 48, and 72 h were generally consistent with the transcriptome data. The transcripts of BmTrypsin-1 and BmACSS3 were significantly increased from 24 to 72 h after BmNPV infection that they may be involved in the maturation process in the latter half of silkworm fifth instar larvae. These findings will help to address the interactions between BmNPV infection and host developmental response.
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Project description:We identified genes regulated by parasitization of the silkworm Bombyx mori by three tachinid parasitoid species, Exorista japonica, Drino inconspicuoides and Pales pavida, using oligonucleotide microarrays. The numbers of genes and their intensity of expression varied with the species of parasitoid, within silkworm hemocytes and fat body. Bombyx mori hemocyte, silkgland and fat body samples parasitizated by Exorista japonica, Drino inconspicuoides and Pales pavida were prepared. Gene expression was compared in these two groups: control and parasitized.
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Project description:We identified genes regulated by parasitization of the silkworm Bombyx mori by three tachinid parasitoid species, Exorista japonica, Drino inconspicuoides and Pales pavida, using oligonucleotide microarrays. The numbers of genes and their intensity of expression varied with the species of parasitoid, within silkworm hemocytes and fat body.
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Project description:Molecular genetic studies of Bombyx mori have led to profound advances in understanding the regulation of development. Bombyx mori brain, as a main endocrine organ, plays important regulatory roles in various biological processes. The microarray technology will allow the genome-wide analysis of gene expression patterns in silkworm brains. We reported microarray-based gene expression profiles in silkworm brains at four stages including V7, P1, P2 and P3. A total of 4,550 genes were transcribed in at least one selected stage. Of these, clustering algorithms separated the expressed genes into stable expressed genes and variable expressed genes. The results of the gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analysis of stable expressed genes showed that the ribosomal and oxidative phosphorylation pathways were principal pathways. Secondly, four clusters of genes with significantly different expression patterns were observed in the 1,175 variable expressed genes. Thirdly, thirty-two neuropeptide hormones genes, nine neuropeptide-like precursor genes, and 117 cuticular protein genes were expressed in selected developmental stages. The present study defined major characteristics of the transcriptional profiles in the brains of Bombyx mori at the specific development stages. Our data will provide abundant information that will be useful in future research.
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Project description:Microsporidia have attracted much attention because they infect a variety of species ranging from protists to mammals, including immunocompromised patients with AIDS or cancer. Aside from the study on Nosema ceranae, few works have focused on elucidating the mechanism in host response to microsporidia infection. Nosema bombycis is a pathogen of silkworm pM-CM-)brine that causes great economic losses to the silkworm industry. Detailed understanding of the host (Bombyx mori) response to infection by N. bombycis is helpful for prevention of this disease. The 23 K silkworm genome array was used to investigate host responses (i.e., Bombyx mori) occurring at 2, 4, 6 and 8 d post-infection by Nosema bombycis.We focused on elucidating the mechanism of the host response to microsporidia infection, especially for the investigation of host immune response . The third instar molted silkworm larvae were in oral infected by Nosema bombycis. In order to known the silkworm host response to Nosema bombycis infection at different time points, samples of infected larvae (i.e., the treatment set) and uninfected larvae (i.e., the control set) were collected at 2, 4, 6 and 8 dpi for RNA extraction and array hybridization. The obtained data were usd to investigate on the interplay of the genome-wide expression profile of hosts.
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Project description:Molecular genetic studies of Bombyx mori have led to profound advances in understanding the regulation of development. Bombyx mori brain, as a main endocrine organ, plays important regulatory roles in various biological processes. The microarray technology will allow the genome-wide analysis of gene expression patterns in silkworm brains. We reported microarray-based gene expression profiles in silkworm brains at four stages including V7, P1, P2 and P3. A total of 4,550 genes were transcribed in at least one selected stage. Of these, clustering algorithms separated the expressed genes into stable expressed genes and variable expressed genes. The results of the gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analysis of stable expressed genes showed that the ribosomal and oxidative phosphorylation pathways were principal pathways. Secondly, four clusters of genes with significantly different expression patterns were observed in the 1,175 variable expressed genes. Thirdly, thirty-two neuropeptide hormones genes, nine neuropeptide-like precursor genes, and 117 cuticular protein genes were expressed in selected developmental stages. The present study defined major characteristics of the transcriptional profiles in the brains of Bombyx mori at the specific development stages. Our data will provide abundant information that will be useful in future research. Transcription profiling experiments, 4 developmental stages (samples) were analyzed. Dual-channel experiments, with test samples labeled by Cy5 and common reference samples labeled by Cy3. Common reference sample was used for data normalization. One Biological replicate. No dye-swaps.
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