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ScComplete-Seq Reveals Comperehensive Picture of Transcriptome

ABSTRACT: scComplete-Seq Reveals Comperehensive Picture of Transcriptome

PROVIDER: PRJNA1086795 | ENA |

REPOSITORIES: ENA

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scComplete-Seq Reveals Comperehensive Picture of Transcriptome

Project description:Many of the underlying mechanisms of intercellular gene expression heterogeneity are still unknown despite the advancements in single-cell transcriptomics. One of the reasons is the partial detection of non-coding RNA types due to their small size and lack of polyadenylation. The ability to detect gene expression dynamics comprehensively would shed light on the regulation and disease-leading dysregulation in a cell-specific manner, and contribute to the discovery of biomarkers and novel therapeutics. We developed scComplete-seq, a single cell assay that enables concurrent profiling of total RNA. After successful integration of it on available high-throughput single-cell platforms, we validated it on cancer cell lines and applied it to peripheral blood mononuclear cells (PBMCs). This unveiled the distinct regulation of tRNAs, mtRNAs and enhancer RNA in monocytes, T and B cells upon Lipopolysaccharide (LPS) and PMA/Ionomycin stimulation compared to resting cells.

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Nascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation

Project description:This SuperSeries is composed of the following subset Series: GSE36871: Nascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation [RNA-Seq] GSE36872: Nascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation [Nascent-Seq] GSE36873: Nascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation [StrandSpe_NascentSeq] GSE36874: Nascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation [ChIP-seq] Refer to individual Series

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Project description:This SuperSeries is composed of the following subset Series: GSE27967: ChIP-seq analysis reveals distinct H3K27me3 profiles associated with gene regulation [ChIP-seq] GSE27969: ChIP-seq analysis reveals distinct H3K27me3 profiles associated with gene regulation [mRNA profiling] Refer to individual Series

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Seeing the whole transcriptomics picture: Spatial gene expression analysis reveals photoreceptor stress as modulator of retinal vascular changes

Project description:Seeing the whole transcriptomics picture: Spatial gene expression analysis reveals photoreceptor stress as modulator of retinal vascular changes

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mRNA-Seq reveals complex patterns of gene regulation and expression in the mouse skeletal muscle transcriptome associated with calorie restriction

Project description:Sarcopenia is an age-associated loss of skeletal muscle mass and strength that increases the risk of disability. Calorie restriction (CR), the consumption of fewer calories while maintaining adequate nutrition, mitigates sarcopenia and many other age-related diseases. To identify potential mechanisms by which CR preserves skeletal muscle integrity during aging, we used mRNA-Seq for deep characterization of gene regulation and mRNA abundance in skeletal muscle of old mice compared with old mice subjected to CR. mRNA-Seq revealed complex CR-associated changes in expression of mRNA isoforms, many of which occur without a change in total message abundance and thus would not be detected by methods other than mRNA-Seq. Functional annotation of differentially expressed genes reveals CR-associated upregulation of pathways involved in energy metabolism and lipid biosynthesis, and downregulation of pathways mediating protein breakdown and oxidative stress, consistent with earlier microarray-based studies. CR-associated changes not noted in previous studies involved downregulation of genes controlling actin cytoskeletal structures and muscle development. These CR-associated changes reflect generally healthier muscle, consistent with CR’s mitigation of sarcopenia. mRNA-Seq generates a rich picture of the changes in gene expression associated with CR, and may facilitate identification of genes that are primary mediators of CR’s effects. Comprehensive survey of mRNA from skeletal muscle of mice subjected to calorie restricted or control diets using deep sequencing

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KARR-seq reveals principles of high-order ribonucleoprotein structure assembly

Project description:We designed KARR-seq, which reveals RNA-RNA interactions transcriptome-wide. The frequency of KARR-seq chimeras accurately reveals the physical distances between RNAs in vivo. Using KARR-seq, we systematically analyzed celullar effect on RNA-RNA interactions.

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Transcriptome analysis of reticulated platelets reveals a prothrombotic profile [mRNA-Seq]

Project description:Transcriptome analysis of reticulated platelets reveals a prothrombotic profile [mRNA-Seq]

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