Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1162771 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30721534_1.fastq.gz | Fastqsanger.gz | |||
| SRR30721534_2.fastq.gz | Fastqsanger.gz | |||
| SRR30721535_1.fastq.gz | Fastqsanger.gz | |||
| SRR30721535_2.fastq.gz | Fastqsanger.gz | |||
| SRR30721536_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 30 |
Similar Datasets
Project description:RNA-seq of BmNPV cells infected by indicated mutant BmNPV to determine the impact on viral gene expression of the cis-interacting sites on BmNPV by knocking out them via RED system
2024-10-01 | GSE278147 | GEO
Project description:Ubiquitin-fold modifier 1 (UFM1) is attached to protein substrates through the sequential activity of an E1 (UBA5)-E2 (UBC1)-E3 (UBL1) cascade. UFBP1 is a conserved UFL1-interacting protein in mammals. However, there is no study on UFBP1 in silkworm yet. In this study, we identified a UFBP1 ortholog in B. mori genome. Spatio-Temporal expression profiles showed that BmUFBP1 expression was highly in midgut, fatbody, and at the moth stage. BmUFBP1 knockdown inhibited ER-stress induced ER chaperone expression and BmNPV proliferation, while BmUFBP1 overexpression increased BmNPV proliferation. Furthermore, RNA sequencing and experimental verification identified the HSP70 family member BmBIP as the BmUFBP1 downstream target in regulating BmNPV proliferation. Overall, these results suggest that BmUFBP1 facilitates BmNPV proliferation via ATF6-BIP signaling.
2024-07-31 | GSE272804 | GEO
Project description:Transcription factors (TFs) influence cell function by interpreting information contained within cis-regulatory elements in chromatin. Whereas ChIP-sequencing has been used to identify and map transcription factor-DNA interactions, it has been difficult to assign functionality to the binding sites identified. Thus, in this study we probed the transcriptional activity, DNA-binding competence and functional activity of select nuclear receptor (NR) mutants in cellular and animal model systems and used this information to define the sequence constraints of functional steroid nuclear receptor (sNR) cis-regulatory elements. Analysis of the architecture within sNR chromatin interacting sites revealed that only a small fraction of all sNR chromatin interacting events are associated with transcriptional output, and that this functionality is restricted to elements that vary from the consensus palindromic elements by one or two nucleotides. These findings define the transcriptional grammar necessary to predict functionality from linear genome sequences.
2017-04-01 | GSE94737 | GEO
Project description:The molecular mechanism involved in BmNPV resistance was investigated using a genome wide microarray in the midgut tissues of BmNPV infected resistant (Sarupat) and susceptible (CSR-2) Indian silkworm races. In the resistant race, 735 genes were upregulated and 589 genes were down regulated at 12 hours of BmNPV post infection. Similarly in case of susceptible race, 2183 genes were up regulated and 2115 genes were down regulated. Among the differentially expressed genes, nine upregulated and eight down regulated genes were validated using real time qPCR analysis. In Sarupat, the significantly upregulated genes are vacuolar protein sorting associated gene, X fin like protein and Carboxy peptidase E like protein in BmNPV infected midguts, whereas the prominent down regulated genes are glutamate receptor ionotropic kainite 2-like, BTB/POZ domain and transferrin. In the case of CSR-2, the considerably upregulated genes are Peptidoglycan recognition protein S6 precursor and rapamycin while the conspicuous down regulated genes are facilitated trehalose transporter and zinc transporter ZIP1-like gene. Our results provided a vital insights of Bombyx mori in reference with its molecular mechanism in immune response against the BmNPV invasion. Organism : Bombyx mori , Agilent Custom Silkworm Gene Expression 4x44k Array (AMADID: 066047) designed by Genotypic Technology Private Limited.
2016-07-01 | E-GEOD-71240 | biostudies-arrayexpress
Project description:The molecular mechanism involved in BmNPV resistance was investigated using a genome wide microarray in the midgut tissues of BmNPV infected resistant (Sarupat) and susceptible (CSR-2) Indian silkworm races. In the resistant race, 735 genes were upregulated and 589 genes were down regulated at 12 hours of BmNPV post infection. Similarly in case of susceptible race, 2183 genes were up regulated and 2115 genes were down regulated. Among the differentially expressed genes, nine upregulated and eight down regulated genes were validated using real time qPCR analysis. In Sarupat, the significantly upregulated genes are vacuolar protein sorting associated gene, X fin like protein and Carboxy peptidase E like protein in BmNPV infected midguts, whereas the prominent down regulated genes are glutamate receptor ionotropic kainite 2-like, BTB/POZ domain and transferrin. In the case of CSR-2, the considerably upregulated genes are Peptidoglycan recognition protein S6 precursor and rapamycin while the conspicuous down regulated genes are facilitated trehalose transporter and zinc transporter ZIP1-like gene. Our results provided a vital insights of Bombyx mori in reference with its molecular mechanism in immune response against the BmNPV invasion.
2016-07-01 | GSE71240 | GEO
Project description:To investigate the transcriptional regulatory role of the transcription factor BmGATA, and the impact of BmNPV infection on its activation capacity
2024-10-01 | GSE278146 | 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.
2021-03-02 | GSE167875 | GEO
Project description:Bombyx mori is one of the key lepidopteran model species, and is economically important for silk production and proteinaceous drug expression. Baculovirus and insect host are important natural biological models for studying host-pathogen interactions. The impact of Bombyx mori nucleopolyhedrovirus (BmNPV) infection on the proteome and acetylome of Bombyx mori ovarian (BmN) cells were explored to facilitate a better understanding of infection-driven interactions between BmNPV and host in vitro. The proteome and acetylome were profiled through 6-plex Tandem mass tag (TMT) labelling-based quantitative proteomics. Totally, 4,194 host proteins were quantified, of which 33 were up-regulated and 47 were down-regulated in BmN cells at 36 h post-infection. Based on the proteome, quantifiable differential Kac proteins were identified and functionally annotated to gene expression regulation, energy metabolism, substance synthesis and metabolism after BmNPV infection. Altogether, 644 Kac sites in 431 host proteins and 39 Kac sites in 22 viral proteins were identified and quantified in infected BmN cells. Our study demonstrated that BmNPV infection globally impacts the proteome and acetylome of BmN cells. The viral proteins are also acetylated by the host acetyltransferase. Protein acetylation is essential for cellular self-regulation and response to virus infection. This study provides new insights for understanding the host-virus interaction mechanisms, and the role of acetylation in BmN cellular response to viral infection.
2017-11-27 | PXD008054 | Pride
Project description:As the most widely used mammalian model organism, mice play a critical role in biomedical research for mechanistic study of human development and diseases. Today, functional sequences in the mouse genome are still poorly annotated a decade after its initial sequencing. We report here a map of nearly 300,000 cis-regulatory sequences in the mouse genome, representing active promoters, enhancers and CTCF binding sites in a diverse set of 19 tissues and cell types. This map provides functional annotation to nearly 11% of the genome, and over 70% of conserved, non-coding sequences. We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we demonstrate that cis-regulatory sequences are organized into domains of coordinately regulated enhancers and promoters. Our results provide a valuable resource for the annotation of functional elements in the mammalian genome, and study of regulatory mechanisms for tissue-specific gene expression. 19 tissues and primary cell types were examined.
2012-07-01 | E-GEOD-29218 | biostudies-arrayexpress