Bombycoidea
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR179498_1.fastq.gz | Fastqsanger.gz | |||
| DRR179498_2.fastq.gz | Fastqsanger.gz | |||
| DRR179499_1.fastq.gz | Fastqsanger.gz | |||
| DRR179499_2.fastq.gz | Fastqsanger.gz | |||
| DRR179500_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptional characteristics of genes in the fat body of domestic silkworms after 24 h exposure to phoxim through whole-genome oligonucleotide microarray. Transcriptional profiling of fat body in the domestic silkworms comparing control untreated fat body with phoxim-treated fat body Transcription profiling experiments, phoxim-treated fat body (samples) were analyzed. Dual-channel experiments, with test samples labeled by Cy5 and control samples labeled by Cy3. Three Biological replicate. No dye-swaps.
2016-07-03 | E-GEOD-60877 | biostudies-arrayexpress
Project description:Transcriptional characteristics of genes in the fat body of domestic silkworms after 24 h exposure to phoxim through whole-genome oligonucleotide microarray.
2016-01-01 | GSE60877 | GEO
Project description:Single-base resolution DNA methylomes have been accomplished for both Arabidopsis and human cells which have high genome methylation levels by Illumina ultra-high-throughput bisulfite sequencing technology (MethylC-Seq). Here by combining MethylC-Seq and biological replicate strategies we generated single-base resolution methylome for the silkworm which has low genome methylation levels like other insects. Our conservative estimation showed that methylcytosines (mCs) accout for about 0.11% of genomic cytosines, exclusively in CG context. The CG methylation is significantly enriched in gene bodies and positively correlated with gene expression levels, suggesting its positive role in gene transcription in silkworms. However, the well-documented functions of methylation on promoters and rDNAs in plants and mammals do not seem to have effects in insects. Methylated genes are enriched in functions involved in cellular metabolism and biosynthesis. Small RNA (smRNA) loci are also significantly enriched in gene bodies, and moreover, the smRNA loci and the predicted target sites of microRNA have high level of CG methylation, indicating functional involvement of smRNAs in the genic methylation This first methylome for silkworms provides a foundation for further studies on the epigenetic gene regulation of silkworms’ or even insects’ gene methylation. Each silk gland of 5th instar larvae of two individuals (called Biological Replicate 1 and 2, respectively) of the silkworm (Bombyx mori) strain Dazao was ground into powder in liquid nitrogen. Half of the powder from each silk gland was used to extract total DNAs using DNeasy Blood & Tissue Kit (Qiagen) and another half was used to extract total RNAs using RNeasy Mini Kit (Qiagen). We sequenced bisulfite-treated total DNA extracted from the silk glands of the two individuals, using Illumina Ultra-High-Throughput Sequencing, generating the Single-Base Resolution Methylomes. To reveal functional consequences of gene body methylation, we generated expression profiles for the two individuals’ silk glands using Digital Gene Expression tag profiling (DGE) technology, which combines classic SAGE (Serial Analysis of Gene Expression) and Illumina ultra-high-throughput sequencing technology.
2010-04-09 | E-GEOD-18315 | biostudies-arrayexpress
Project description:Helicobacter pylori, which is known as pathogens of various gastric diseases, have many types of genome sequence variants. That is part of the reason why pathogenesis and infection mechanisms of the H. pylori-driven gastric diseases have not been well clarified yet. Here we performed a large-scale proteome analysis to profile the heterogeneity of the proteome expression of 7 H. pylori strains by using LC/MS/MS-based proteomics approach combined with a customized database consisting of non-redundant tryptic peptide sequences derived from full genome sequences of 52 H. pylori strains. The non-redundant peptide database enabled us to identify more peptides in the database search of MS/MS data, compared with a simply merged protein database. Using the approach we performed proteome analysis of genome-unknown strains of H. pylori in as large-scale as genome-known ones. Clustering of the H. pylori strains using the proteome profiling slightly differed from the genome profiling and more clearly divided the strains into two groups based on the isolated area. Furthermore, we also identified phosphorylated proteins and sites of the H. pylori strains and obtained phosphorylation motif located in the N-terminus, which are commonly observed in bacteria.
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Project description:In this study, we have applied the top-down approach to reduce the genome of B. subtilis in order to obtain minimal strains with robust growth on complex medium at 37°C. For this purpose, we have evaluated the function of each gene of the B. subtilis genome and identified essential, important and dispensable genomic regions. Using an efficient markerless and scarless deletion method and a system allowing induction of genetic competence in the complete cell population, we have constructed two genome-reduced strains lacking about 36% of dispensable genetic information. Multi-omics analyses with the genome-reduced strains revealed substantial changes in the transcriptome, the proteome and in the metabolome. The massive reorganization of metabolism in the two genome-reduced strains can be explained by the underlying genotypes that were determined by genome re-sequencing. Moreover, the transcriptome and proteome analyses uncovered novel dispensable genomic regions that can be removed to further streamline the B. subtilis genome. In conclusion, both minimal strains show interesting metabolic features and they serve as excellent starting points to generate an ultimate reduced-genome B. subtilis cell containing only genes required for robust growth on complex medium.
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Project description:Transcriptional characteristics of genes in the midgut of domestic silkworms after 24 h exposure to phoxim through whole-genome oligonucleotide microarray.
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Project description:Single-base resolution DNA methylomes have been accomplished for both Arabidopsis and human cells which have high genome methylation levels by Illumina ultra-high-throughput bisulfite sequencing technology (MethylC-Seq). Here by combining MethylC-Seq and biological replicate strategies we generated single-base resolution methylome for the silkworm which has low genome methylation levels like other insects. Our conservative estimation showed that methylcytosines (mCs) accout for about 0.11% of genomic cytosines, exclusively in CG context. The CG methylation is significantly enriched in gene bodies and positively correlated with gene expression levels, suggesting its positive role in gene transcription in silkworms. However, the well-documented functions of methylation on promoters and rDNAs in plants and mammals do not seem to have effects in insects. Methylated genes are enriched in functions involved in cellular metabolism and biosynthesis. Small RNA (smRNA) loci are also significantly enriched in gene bodies, and moreover, the smRNA loci and the predicted target sites of microRNA have high level of CG methylation, indicating functional involvement of smRNAs in the genic methylation This first methylome for silkworms provides a foundation for further studies on the epigenetic gene regulation of silkworms’ or even insects’ gene methylation.
2010-04-09 | GSE18315 | GEO
Project description:DNA replication must be tightly controlled during each cell cycle to prevent unscheduled replication and ensure proper genome maintenance. The currently known controls that prevent re-replication act redundantly to inhibit pre-Replicative Complex (pre-RC) assembly outside of the G1 phase of the cell cycle. We have analyzed the effects of re-replication on the S. cerevisiae genome using a combination of Comparitive Genomic Hybridization (CGH) of re-replicating strains and Genome-Wide Location Analysis of pre-RC components. These data indicate which sites in the genome assemble pre-RCs under re-replication conditions, which sites undergo re-initiation and the extent of re-replication. Keywords: comparative genomic hybridization, ChIP-chip, re-replication, DNA replication, pre-RC
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Project description:We have combined standard micrococcal (MNase) digestion of nuclei with a modified protocol for construction paired-end DNA sequencing libraries to map both nucleosomes and subnucleosome-sized particles at single base-pair resolution throughout the budding yeast genome. We found that partially unwrapped nucleosomes and subnucleosome-sized particles can occupy the same position within a cell population, suggesting dynamic behavior. By varying the time of MNase digestion, we have been able to observe changes that reflect differential sensitivity of particles, including eviction of nucleosomes. Our protocol and mapping method provide a general strategy for characterizing full epigenomes. We used micrococcal nuclease mapping, chromatin immunoprecipitation and paired-end sequencing to determine the structure of yeast centromeres at single base-pair resolution.
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