Ontology highlight
ABSTRACT:
PROVIDER: PRJNA601168 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10898400_1.fastq.gz | Fastqsanger.gz | |||
| SRR10898400_2.fastq.gz | Fastqsanger.gz | |||
| SRR10898700_1.fastq.gz | Fastqsanger.gz | |||
| SRR10898700_2.fastq.gz | Fastqsanger.gz | |||
| SRR10899200_1.fastq.gz | Fastqsanger.gz |
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Project description:To offer a robust and highly characterized three-dimensional (3D) model for anti-cancer drug discovery and basic research, we developed a 3D system in which the immortalized breast cancer cell lines MCF-7 and MDA-MB-231 were grown in recombinantly produced spider silk functionalized with the cell adhesion motif from fibronectin (FN-silk). The aim of this study is to evaluate whole-transcriptome changes driven by growth in such 3D model.
2023-09-13 | GSE209570 | GEO
Project description:Human pluripotent stem cells (hPSCs) are intrinsically able to self-organize into cerebral organoids that mimic features of developing human brain tissue. These three-dimensional (3D) structures provide a unique opportunity to generate cytoarchitecture and cell-cell interactions reminiscent of human brain complexity in a dish. However, current in vitro brain organoid methodologies often result in intra-organoid variability, limiting their use in recapitulating later developmental stages as well as in disease modeling and drug discovery. In addition, cell stress and hypoxia resulting from long-term culture lead to incomplete maturation and cell death within the inner core. Here, we used a recombinant silk microfiber network as a scaffold to drive human PSCs to self-arrange into engineered cerebral organoids. Silk scaffolding promoted neuroectoderm formation and reduced heterogeneity of cellular organization within individual organoids. Bulk and single cell transcriptomics confirmed that silk cerebral organoids display more homogeneous and functionally mature neuronal properties than organoids grown in the absence of silk fibers. Furthermore, oxygen sensing analysis showed that silk scaffolds create more favorable growth and differentiation conditions by facilitating the delivery of oxygen and nutrients. Silk-engineering platform appears to reduce intra-organoid variability and enhances functional maturation during spontaneous self-patterning in human brain organoid differentiation.
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Project description:Human pluripotent stem cells (hPSCs) are intrinsically able to self-organize into cerebral organoids that mimic features of developing human brain tissue. These three-dimensional (3D) structures provide a unique opportunity to generate cytoarchitecture and cell-cell interactions reminiscent of human brain complexity in a dish. However, current in vitro brain organoid methodologies often result in intra-organoid variability, limiting their use in recapitulating later developmental stages as well as in disease modeling and drug discovery. In addition, cell stress and hypoxia resulting from long-term culture lead to incomplete maturation and cell death within the inner core. Here, we used a recombinant silk microfiber network as a scaffold to drive human PSCs to self-arrange into engineered cerebral organoids. Silk scaffolding promoted neuroectoderm formation and reduced heterogeneity of cellular organization within individual organoids. Bulk and single cell transcriptomics confirmed that silk cerebral organoids display more homogeneous and functionally mature neuronal properties than organoids grown in the absence of silk fibers. Furthermore, oxygen sensing analysis showed that silk scaffolds create more favorable growth and differentiation conditions by facilitating the delivery of oxygen and nutrients. Silk-engineering platform appears to reduce intra-organoid variability and enhances functional maturation during spontaneous self-patterning in human brain organoid differentiation.
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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:P1 is the major QTL for maysin and chlorogenic acid accumulation in silk. Both compounds were important for plant defenses. Silk is an important reproductive organ that is critical for good seed setting in corn ear and needs to be protected against various stresses, therefore, metabolics compounds (ex: phenolics) were highly enriched in silk. Here we characterize transcriptome changes in maize protoplast, and natural variants of P1 silks, and pericards to characterize the regulatory landscape. Also we evaluated profiles of silk in B73 x A632 hybrids in order to cis and trans specific effect driven by P1 in maize. Our study identifies new P1 targets in the silk and protoplast. Together with the RNA-seq data (P1-rr vs P1-ww in silk and pericarp and protoplast 35S:P1 vs empty vector control), we observed new P1 functions in silk that were not observed in pericarp. Also, Protoplast and silk ChIP-seq in F1 silk, as well as DAP-seq analysis of P1 - shows specific P1 targets with highlight cis and trans effect on the F1 hybrids.
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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.
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Project description:Spider silk synthesis is an emerging model for the evolution of tissue-specific gene expression and the role of gene duplication in functional novelty, but its potential has not been fully realized. Accordingly, we quantified transcript (mRNA) abundance in seven silk gland types and three non-silk gland tissues for three cobweb-weaving spider species. Evolutionary analyses based on expression levels of thousands of homologous transcripts and phylogenetic reconstruction of 605 gene families demonstrated conservation of expression for each gland type among species. Despite serial homology of all silk glands, the expression profiles of the glue-forming aggregate glands were divergent from fiber-forming glands. Also surprising was our finding that shifts in gene expression among silk gland types were not necessarily coupled with gene duplication, even though silk-specific genes belong to multi-paralog gene families. Our results challenge widely accepted models of tissue specialization and significantly advance efforts to replicate silk-based high-performance biomaterials.
2017-08-23 | GSE95367 | GEO
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:In this study, RNA-seq based comparative transcriptome analysis was used to study the genetic response of maize silk to pollen tube penetration and in comparison to the fungal invasion of Fusarium graminearum and Ustilago maydis. RNA-seq libraries of 8 tissues were generated from leaf, root, seed, pollen tube, silk, pollinated silk, infected silk with Fusarium and infected silk with Ustilago.
2019-03-17 | E-MTAB-4559 | biostudies-arrayexpress
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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