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Protecting RNA Integrity for Spatial Transcriptomics While Improving Immunofluorescent Staining Quality

ABSTRACT: Protecting RNA Integrity for Spatial Transcriptomics While Improving Immunofluorescent Staining Quality

PROVIDER: PRJNA951864 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24058249_1.fastq.gz	Fastqsanger.gz
	SRR24058249_2.fastq.gz	Fastqsanger.gz
	SRR24058250_1.fastq.gz	Fastqsanger.gz
	SRR24058250_2.fastq.gz	Fastqsanger.gz
	SRR24058251_1.fastq.gz	Fastqsanger.gz

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Protecting RNA Integrity for Spatial Transcriptomics While Improving Immunofluorescent Staining Quality

Project description:In comparison to bulk sequencing or single cell sequencing, spatial transcriptomics preserves the spatial information in tissue slices and can even be mapped to immunofluorescent stainings. This enables to unravel complex interactions of neighboring cells or to link cell morphology to transcriptome data. The 10x genomics visium spatial assay offers to combine spatial transcriptomics with immunofluorescent staining of cryo-sectioned tissue slices. We applied this technique to 10 µm fresh frozen mouse brain slices and developed a protocol that still protects RNA integrity while improving buffers for immunofluorescent staining. We investigated the influence of various parameters on RNA integrity and on antibody binding of blocking, staining as well as wash buffers. Finally, we propose a protocol that does not alter RNA integrity in comparison the 10x genomics demonstrated protocol but allows the usage of several antibodies that have not been compatible with the protocol before. In addition, we discuss the influence of the tested parameters which offers further development of application specific staining protocols.

2023-06-07 | GSE228891 | GEO

Improving coriander yield and quality with a beneficial bacterium

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Improving coriander yield and quality with a beneficial bacterium

Project description:Plant growth-promoting rhizobacteria (PGPR) are soil microbes that can promote plant growth and/or increase plant resistance to one or multiple stress conditions. These natural resources are environmentally friendly tools for reducing the use of chemical fertilizers and pesticides and for improving the nutritional quality of plants, including pharmacological metabolites. Coriander (Coriandrum sativumL.), commonly known as cilantro or Chinese parsley, is a worldwide culinary and medicinal plant with both nutritional and medicinal properties. Little is known about how PGPR may promote plant growth or affect metabolite profiles in coriander. Here, by usingAeromonassp. H1 that is a PGPR strain, we investigate how coriander yield and quality could be affected by PGPR with transcriptome insights.

2024-03-11 | GSE247080 | GEO

IMiQ: a novel protein quality control compartment protecting mitochondrial functional integrity.

Project description:Aggregation processes can cause severe perturbations of cellular homeostasis and are frequently associated with diseases. We performed a comprehensive analysis of mitochondrial quality and function in the presence of aggregation-prone polypeptides. Despite a significant aggregate formation inside mitochondria, we observed only a minor impairment of mitochondrial function. Detoxification of aggregated reporter polypeptides as well as misfolded endogenous proteins inside mitochondria takes place via their sequestration into a specific organellar deposit site we termed intramitochondrial protein quality control compartment (IMiQ). Only minor amounts of endogenous proteins coaggregated with IMiQ deposits and neither resolubilization nor degradation by the mitochondrial protein quality control system were observed. The single IMiQ aggregate deposit was not transferred to daughter cells during cell division. Detoxification of aggregates via IMiQ formation was highly dependent on a functional mitochondrial fission machinery. We conclude that the formation of an aggregate deposit is an important mechanism to maintain full functionality of mitochondria under proteotoxic stress conditions.

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RNA quality control by CCR4 safeguards chromatin integrity and centromere function in Arabidopsis [RNA-seq]

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Project description:RNA quality control by CCR4 safeguards chromatin integrity and centromere function in Arabidopsis [ChIP-seq]

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RNA quality control by CCR4 safeguards chromatin integrity and centromere function in Arabidopsis [EM-seq]

Project description:RNA quality control by CCR4 safeguards chromatin integrity and centromere function in Arabidopsis [EM-seq]

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RNA quality control by CCR4 safeguards chromatin integrity and centromere function in Arabidopsis [smallRNA-seq]

Project description:RNA quality control by CCR4 safeguards chromatin integrity and centromere function in Arabidopsis [smallRNA-seq]

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RNA quality control by CCR4 safeguards chromatin integrity and centromere function in Arabidopsis [EM-seq]

Project description:The centromere is a pivotal chromatin domain that ensures accurate chromosome segregation during cell division. However, the epigenome regulation of the centromere and its impact on centromere function remain largely elusive. Here in the model plant Arabidopsis, we show that CCR4, the catalytic subunit of the RNA deadenylation complex CCR4-NOT, is essential for maintenance of the centromere epigenome and chromosome integrity. We demonstrate that CCR4 is involved in shortening of the poly(A) tails of transcripts originated from centromeric transposons and repeats, thereby promoting the production of small interfering RNAs (siRNAs). The CCR4-dependent siRNAs guide non-CG DNA methylation at centromere repeats, and CCR4 cooperates with canonical DNA methylation pathways to enhance centromeric H3K9 methylation and ensure mitotic chromosome stability. Our study illustrates the crucial role of RNA quality control in RNA interference and reveals the elaborate mechanism that safeguards plant centromeres through epigenomic regulation.

2024-08-24 | GSE274196 | GEO

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