Ontology highlight
ABSTRACT:
PROVIDER: PRJNA933185 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23385163_1.fastq.gz | Fastqsanger.gz | |||
| SRR23385163_2.fastq.gz | Fastqsanger.gz | |||
| SRR23385164_1.fastq.gz | Fastqsanger.gz | |||
| SRR23385164_2.fastq.gz | Fastqsanger.gz | |||
| SRR23385165_1.fastq.gz | Fastqsanger.gz |
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Project description:The silk gland development has a greater impact on silk yields in silkworms. Silk glands from three pure silkworm strains (A798, A306, and XH) with different silk gland weight phenotypes were compared using transcriptome, proteomics, and WGCNA. Five genes (BGIBMGA002524, BGIBMGA002629, BGIBMGA005659, BGIBMGA005711, and BGIBMGA010889) may be strongly associated with the growth of silk glands to be confirmed. These DEGs encoded alkylglycerol monooxygenase (AGMO), glucose dehydrogenase (GDH), zonadhesin (ZAN), odorant binding protein (OBPs), and β-fructofuranosidase (INV), respectively. PCR and ELISA were used to verify the mRNA and protein expression of five genes in the silk glands and tissues of 18 silkworm strains. The GO results showed that four genes have higher levels of expression and participate in glycogen metabolism, fatty acid synthesis, and branched-chain amino acid metabolism, thus, promoting growth and silk proteins synthesis.
2023-08-02 | GSE239380 | GEO
Project description:We collected a total of 9.8 million mass spectra data generated in the laboratory from the proteomics analyses of different silkworm tissues, including the posterior silk gland 29, middle silk gland 30, ovary and testis 31, head 32, brain, prothoracic glands, subesophageal ganglion 33, hemolymph 34, fat body 35 and embryo 36,37 of domestic silkworm, and the posterior silk gland of wild silkworm 38.
2019-07-01 | PXD009672 | Pride
Project description:We collected a total of 9.8 million mass spectra generated in the laboratory from the proteomics analyses of different silkworm tissues, including the posterior silk gland (PSG) 30, middle silk gland 31, ovary and testis 32, head 33, brain, prothoracic glands, subesophageal ganglion 34, hemolymph 35, fat body 36 and embryo 37,38 of domestic silkworm, and the posterior silk gland of wild silkworm 39.
2019-07-01 | PXD009697 | Pride
Project description:We collected a total of 9.8 million mass spectra data generated in the laboratory from the proteomics analyses of different silkworm tissues, including the posterior silk gland (29), middle silk gland (30), ovary and testis (31), head (32), brain, prothoracic glands, subesophageal ganglion (33), hemolymph (34), fat body (35) and embryo (36,37) of domestic silkworm, and the posterior silk gland of wild silkworm (38).
2019-07-01 | PXD009671 | Pride
Project description:Background: MicroRNA (miRNA) and other small regulatory RNAs contribute to the modulation of a large number of cellular processes. We sequenced three total RNA libraries prepared from the whole body, and the anterior and posterior silk glands of Bombyx mori, with a view to expanding the repertoire of silkworm miRNAs and exploring transcriptional differences in miRNAs between segments of the silk gland. Results: With the aid of large-scale Solexa sequencing technology, we validated 244 unique miRNA genes, including 191 novel and 53 previously reported genes, corresponding to 309 loci in the silkworm genome. Interestingly, 24 unique miRNAs were widely conserved from invertebrates to vertebrates; 12 unique ones were limited to invertebrates and 33 were confined to insects; whereas the majority of the newly identified miRNAs were silkworm-specific. We identified 21 clusters and 42 paralogs of miRNAs in the silkworm genome. However, sequence tags showed that paralogs or clusters are not prerequisites for coordinated transcription and accumulation. The majority of silkworm-specific miRNAs are located in transposable elements, and display significant differences in abundance between the anterior and posterior silk glands. Conclusions: Conservative analysis revealed that miRNAs serve as phylogenetic markers and function in evolutionary signaling. The newly identified miRNAs greatly enriched the repertoire of insect miRNAs, and provide insights into miRNA evolution, biogenesis, and expression in insects. The differential expression of miRNAs in the anterior and posterior silk glands supports their involvement as new layers in the regulation of the silkworm silk gland.
2010-02-01 | GSE17965 | GEO
Project description:Background: MicroRNA (miRNA) and other small regulatory RNAs contribute to the modulation of a large number of cellular processes. We sequenced three total RNA libraries prepared from the whole body, and the anterior and posterior silk glands of Bombyx mori, with a view to expanding the repertoire of silkworm miRNAs and exploring transcriptional differences in miRNAs between segments of the silk gland. Results: With the aid of large-scale Solexa sequencing technology, we validated 244 unique miRNA genes, including 191 novel and 53 previously reported genes, corresponding to 309 loci in the silkworm genome. Interestingly, 24 unique miRNAs were widely conserved from invertebrates to vertebrates; 12 unique ones were limited to invertebrates and 33 were confined to insects; whereas the majority of the newly identified miRNAs were silkworm-specific. We identified 21 clusters and 42 paralogs of miRNAs in the silkworm genome. However, sequence tags showed that paralogs or clusters are not prerequisites for coordinated transcription and accumulation. The majority of silkworm-specific miRNAs are located in transposable elements, and display significant differences in abundance between the anterior and posterior silk glands. Conclusions: Conservative analysis revealed that miRNAs serve as phylogenetic markers and function in evolutionary signaling. The newly identified miRNAs greatly enriched the repertoire of insect miRNAs, and provide insights into miRNA evolution, biogenesis, and expression in insects. The differential expression of miRNAs in the anterior and posterior silk glands supports their involvement as new layers in the regulation of the silkworm silk gland. Sequencing three total RNA pools of the whole silkworm body from 5th-instar day-3 larvae, and anterior and posterior silkworm silk glands, using the latest sequencing Solexa technology
2010-02-01 | E-GEOD-17965 | biostudies-arrayexpress
Project description:The silkworm silk gland is one of the most efficient protein synthesis systems among all organisms. Its amazingly efficient protein synthesis makes the silk gland a desirable object for basic studies on gene expression and regulation and for biotechnological applications. At the early stages of the fifth (final) instar, the cellular structures necessary for the synthesis of fibroin are rapidly formed, and at the later stage the synthesis of fibroin proceeds at a maximum rate. The posterior silk gland (PSG) is the longest suborgan and is responsible for the synthesis of the silk core protein fibroin, which is composed of heavy (H) and light (L) chains plus P25. We used microarrays to detail the global programme of gene expression in silkworm PSG during the late larval stages, including the fourth molting (M4) and day 1 (V1), day 3 (V3), day 5 (V5), and day 7 (wandering stage, W) of the fifth instar, and to reveal the correlations of differential expression genes with the PSG development and fibroin synthesis.
2012-12-05 | GSE26172 | GEO
Project description:The silkworm silk gland is one of the most efficient protein synthesis systems among all organisms. Its amazingly efficient protein synthesis makes the silk gland a desirable object for basic studies on gene expression and regulation and for biotechnological applications. At the early stages of the fifth (final) instar, the cellular structures necessary for the synthesis of fibroin are rapidly formed, and at the later stage the synthesis of fibroin proceeds at a maximum rate. The posterior silk gland (PSG) is the longest suborgan and is responsible for the synthesis of the silk core protein fibroin, which is composed of heavy (H) and light (L) chains plus P25. We used microarrays to detail the global programme of gene expression in silkworm PSG during the late larval stages, including the fourth molting (M4) and day 1 (V1), day 3 (V3), day 5 (V5), and day 7 (wandering stage, W) of the fifth instar, and to reveal the correlations of differential expression genes with the PSG development and fibroin synthesis. Silkworm PSGs were collected at M4, V1, V3, V5, and W stages for RNA extraction and hybridization on 23K Silkworm Genome Arrays (CapitalBio Corp., Beijing, China). Three groups of biological replicates were prepared at each time point.Dual-dye experiments were performed for the PSG at M4, V1, V3, V5, and W; a total of 15 samples were tested including three biological replicates at each stage. Aliquots of each test sample were pooled as a common reference sample (CKA). The test samples and CKA were labeled with Cy3 and Cy5, respectively.
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Project description:Background: The growth and development of the posterior silk gland and the biosynthesis of the silk core protein at the fifth larval instar stage of Bombyx mori are of paramount importance for silk production. Results: Here, aided by next-generation sequencing and microarry assay, we profile 1,229 microRNAs (miRNAs), including 728 novel miRNAs and 110 miRNA/miRNA* duplexes, from the posterior silk gland at the fifth larval instar. Target gene prediction yields 14,222 unique target genes from 1,195 miRNAs. Functional categorization classifies the genes into complex pathways that include both cellular and metabolic processes, especially protein synthesis and processing. Conclusion: The enrichment of target genes in the ribosome-related pathway indicates that miRNAs may directly regulate translation. Our findings pave a way for further functional elucidation of these miRNAs in silk production. Sequencing 10 total RNA samples from the posterior silk gland of different strains and developmental stage using Illumina Solexa technology. Four strains of silkworm (Q, B, QB and BQ) with different two development stages (stage 1: fourth instar molting to day 2 of fifth instar; stage 2: fifth instar day 3 to day 8 before spinning, according to our previous genes expression cluster analysis), and two strains (R1 and J1) from entire period (stage 1 + stage 2).
2014-07-30 | E-GEOD-56380 | biostudies-arrayexpress
Project description:The middle silk gland (MSG) is an important silkworm sub-organ for synthesis and secretion of sericin proteins. To investigate the proteome differences among the anterior, middle, and posterior regions of silkworm MSG at the third day of the fifth instar, the extracted tissue proteins were digested in gel with trypsin followed by shotgun LC-MS/MS analysis with a LTQ-Orbitrap mass spectrometer.
2016-03-11 | PXD003371 | Pride