Squid
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA320263 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Tandem repeat sequencing in XLID
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Project description:Sea-island cotton (Gossypium barbadense L.) has superior fiber quality properties such as length, fineness and strength, while Upland cotton (Gossypium hirsutum L.) is characterized by high yield. To reveal features of Upland cotton and Sea-island cotton fiber cells, differential genes expression profiles during fiber cell elongation and in secondary wall deposits were established using cDNA microarray technology. This research provides a valuable genomic resource to deepen our understanding of the molecular mechanisms of cotton fiber development, and may ultimately lead to improvements in cotton fiber quality and yield. 15 samples were prepared for microarray slides hybridized with three biological replicate samples including a swap-dye experiment for each growth stage. Each spot had a repeat in the microarray slideM-oM-<M-^Ltherefore, data for six replicate experiments performed with biologically independent samples.
2012-05-23 | E-GEOD-18028 | biostudies-arrayexpress
Project description:Ageing compromises the mechanical properties of skin, with increased fragility and coincident slowing of the healing process making aged skin susceptible to chronic wounding. The ageing process is driven by an aggregation of damage to cells and extracellular matrix, compounded by regulatory changes, including age-associated hormonal dysregulation. Here we report on the correlation between mechanical properties and composition of skin from ovariectomised and chronologically aged mice, to assess the extent to which estrogen deprivation drives dermal ageing. We found that age and estrogen abrogation affected skin mechanical properties in contrasting ways: ageing lead to increased tensile strength and stiffness while estrogen deprivation had the opposite effect. Mass spectrometry proteomics showed that the quantity of extractable fibrillar collagen-I decreased with ageing, but no change was observed in ovariectomised mice. This observation, in combination with measurements of tensile strength, was interpreted to reflect changes to the extent of extracellular matrix crosslinking, supported by a significant increase in the staining of advanced glycation endpoints in aged skin. Loss of mechanical strength in the ovariectomy model was consistent with a loss of elastic fibres. Other changes in extracellular matrix composition broadly correlated between aged and ovariectomised mice, indicative of the role of estrogen-related pathways in ageing. This study offers a coherent picture of the relationship between tissue composition and mechanics, but suggests that the deleterious effects of intrinsic skin ageing are compounded by factors beyond hormonal dysregulation.
2019-03-11 | PXD012754 | Pride
Project description:Ageing compromises the mechanical properties of skin, with increased fragility and coincident slowing of the healing process making aged skin susceptible to chronic wounding. The ageing process is driven by an aggregation of damage to cells and extracellular matrix, compounded by regulatory changes, including age-associated hormonal dysregulation. Here we report on the correlation between mechanical properties and composition of skin from ovariectomised and chronologically aged mice, to assess the extent to which estrogen deprivation drives dermal ageing. We found that age and estrogen abrogation affected skin mechanical properties in contrasting ways: ageing lead to increased tensile strength and stiffness while estrogen deprivation had the opposite effect. Mass spectrometry proteomics showed that the quantity of extractable fibrillar collagen-I decreased with ageing, but no change was observed in ovariectomised mice. This observation, in combination with measurements of tensile strength, was interpreted to reflect changes to the extent of extracellular matrix crosslinking, supported by a significant increase in the staining of advanced glycation endpoints in aged skin. Loss of mechanical strength in the ovariectomy model was consistent with a loss of elastic fibres. Other changes in extracellular matrix composition broadly correlated between aged and ovariectomised mice, indicative of the role of estrogen-related pathways in ageing. This study offers a coherent picture of the relationship between tissue composition and mechanics, but suggests that the deleterious effects of intrinsic skin ageing are compounded by factors beyond hormonal dysregulation.
2019-03-11 | PXD012753 | Pride
Project description:Introducing ribosomal tandem repeat barcoding for fungi
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Project description:Short tandem repeat length variants accumulate at high temperatures over generations in Arabidopsis
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Project description:In plants, RNA polymerase II (Pol II) transcription of inverted DNA repeats produces hairpin RNAs that are processed by several DICER-LIKE enzymes into siRNAs that are 21-24-nt in length. When targeted to transcriptional regulatory regions, the 24-nt size class can induce RNA-directed DNA methylation (RdDM) and transcriptional gene silencing (TGS). In a forward genetic screen to identify mutants defective in RdDM of a target enhancer leading to TGS of a downstream GFP reporter gene in Arabidopsis thaliana, we recovered a structurally mutated silencer locus, named SM-NM-^T35S, in which the 35S promoter driving transcription of an inverted repeat of target enhancer sequences had been specifically deleted. Although Pol II-dependent, hairpin-derived 21-24-nt siRNAs were no longer generated at the newly created SM-NM-^T35S locus, the GFP reporter gene was nevertheless still partially silenced. Silencing was associated with methylation in a short tandem repeat in the upstream target enhancer and with low levels of 24-nt tandem repeat siRNAs. Introducing an nrpd1 mutation into the SM-NM-^T35S line fully released GFP silencing and eliminated both the tandem repeat methylation and associated 24-nt siRNAs, demonstrating their dependence on Pol IV. Deletion of the 35S promoter thus revealed a Pol IV-dependent pathway of 24-nt siRNA biogenesis that was previously inhibited or masked by the Pol II-dependent pathway in wild-type plants. Both Pol II- and Pol IV-dependent siRNAs accrued predominantly from cytosine (C)-containing segments of the tandem repeat monomer, suggesting that the local base composition influenced siRNA accumulation. Preferential accumulation of siRNAs at C-containing sequences was also observed at an endogenous tandem repeat comprising discrete C-rich and AT-rich sections. Our studies illuminate the potential complexity of siRNA generation at repeat-containing loci and show that Pol IV can act in siRNA biogenesis in the absence of a conventional Pol II promoter. Examination of whole-genome DNA methylation status in transgenic T+S Arabidopsis plant
2013-05-30 | E-GEOD-47453 | biostudies-arrayexpress
Project description:Tissue mechanical homeostasis, the concept that cells sense mechanical properties and alter rates of ECM synthesis, assembly and degradation, is of broad interest in biology and medicine, but there is little direct support or insight into mechanisms. Tissue mechanical properties such as elasticity and stiffness are determined primarily by the extracellular matrix (ECM). We therefore set out to test the mechanical homeostasis hypothesis by developing mutations in the mechanosensitive protein talin1 that alter cells’ sensing of ECM stiffness. We identified the side-to-side interaction between talin1 rod domain helix bundles 1 and 2 (R1 and R2) as a novel mechanosensitive site. Mutations that decrease the affinity of the interaction result in a leftward shift in cellular stiffness sensing curves, enabling cells to spread and exert tension on softer substrates. Opening of the R1-R2 interface promotes binding of the Arp2/3 subunit ArpC5L, which is required for the altered stiffness sensing. Introduction of these talin mutations into mice resulted in softer tissue in the ascending aorta with less fibrillar collagen and rupture under lower pressure ex vivo. Together, these results demonstrate that altering cellular stiffness sensing results in altered ECM deposition, tissue stiffness and strength, thus providing direct support for the mechanical homeostasis hypothesis. These results also identify a novel mechanosensitive interaction in the talin rod domain that contributes to this mechanism.
2024-07-16 | PXD041630 | Pride