Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1167775 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30857317_1.fastq.gz | Fastqsanger.gz | |||
| SRR30857317_2.fastq.gz | Fastqsanger.gz | |||
| SRR30857318_1.fastq.gz | Fastqsanger.gz | |||
| SRR30857318_2.fastq.gz | Fastqsanger.gz |
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Project description:Genomic analysis of bombyx mori silk Transcriptome
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Project description:To identify functions that distinguish the posterior and median cells producing fibroin and sericin in the silk gland of Bombyx mori, serial analysis of gene expression (SAGE) profiles from both silk gland regions were analyzed and compared. The construction of a B. mori reference tag collection extracted from a set of 38000 Bombyx EST sequenced from the 3’ side, helped annotating the SAGE libraries. Most of the tags appeared at similar relative concentration in the two libraries except for those corresponding to silk proteins that were found region-specific and highly abundant. Strikingly, besides tags from silk protein mRNAs, 19 tags were found in the class of high abundance in the median cell library, which were absent in the posterior cell tag collection. Except tags from SP1 mRNA, no PSG specific tags were found in the same class of abundance. The analysis of MSG-specific different transcripts led to suggest that middle silk gland cell realizes more diversified functions as those already known, of synthesis and secretion of the silk sericins.
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Project description:The silk gland (SG) of the domesticated silkworm Bombyx mori, an economically important insect that has been used for silk production for over 5000 years, is a remarkable organ that produces vast amounts of silk with exceptional properties . Little is known about which SG cells execute silk protein synthesis and its precise spatiotemporal control. Here, we used single-cell RNA-seq to build a comprehensive cell atlas of the B. mori SG, consisting of 14,972 high-quality cells representing 10 distinct cell types, in three early developmental stages. We annotated all 10 cell types and determined their distributions in each region of the SG, decoded their developmental trajectory and gene-switch status, and discovered marker genes involved in the regulation of SG development and silk protein synthesis. Our study reveals the high heterogeneity of B. mori SG cells and their gene expression dynamics for the first time, affording a deeper understanding of silk-producing organs at the single-cell level .
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Project description:Analysis of bombyx mori silk Transcriptome Transcriptome
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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.
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Project description:We report the ATAC-seq data that reveal chromatin accessibility during Bombyx mori development
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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).
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