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SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression.

ABSTRACT: SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression.

OTHER RELATED OMICS DATASETS IN: GSE63266

PROVIDER: PRJNA267121 | ENA |

REPOSITORIES: ENA

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SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression.

Project description:Single-cell mRNA sequencing (RNA-seq) methods have undergone rapid development in recent years, and transcriptome analysis of relevant cell populations at single-cell resolution has become a key research area of biomedical sciences. We here present single-cell mRNA 3-prime end sequencing (SC3-seq), a practical methodology based on PCR amplification followed by 3-prime-end enrichment for highly quantitative, parallel and cost-effective measurement of gene expression in single cells. The SC3-seq allows excellent quantitative measurement of mRNAs ranging from the 10,000-cell to 1-cell level, and accordingly, allows an accurate estimate of the transcript levels by a regression of the read counts of spike-in RNAs with defined copy numbers. The SC3-seq has clear advantages over other typical single-cell RNA-seq methodologies for the quantitative measurement of transcript levels and at a sequence depth required for the saturation of transcript detection. The SC3-seq distinguishes four distinct cell types in the peri-implantation mouse blastocysts. Furthermore, the SC3-seq reveals the heterogeneity in human-induced pluripotent stem cells (hiPSCs) cultured under on-feeder as well as feeder-free conditions, demonstrating a more homogeneous property of the feeder-free hiPSCs. We propose that SC3-seq might be used as a powerful strategy for single-cell transcriptome analysis in a broad range of investigations in biomedical sciences.

2015-03-20 | GSE63266 | GEO

SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression.

Project description: Not available

| S-EPMC4482058 | biostudies-literature

Highly parallel quantification and compartment localization of transcription factors and nuclear proteins

Project description:Transcription factors and other chromatin-associated proteins are difficult to quantify comprehensively. Here we combine facile nuclear sub-fractionation with data-independent acquisition mass spectrometry to achieve rapid, sensitive, and highly-parallel quantification of the nuclear proteome in human cells. We apply this approach to quantify the response to acute degradation of BET bromodomains, revealing unexpected chromatin regulatory dynamics. The method is simple and enables systems-level study of previously inaccessible chromatin and genome regulators.

2020-02-17 | GSE140325 | GEO

Anti-oxidation metabolism measurement in mammalian cells and tissues by quantitative LC/MS method (VI)

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Anti-oxidative metabolism measurement in mammalian cells and tissues by quantitative LC/MS method (IV)

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Anti-oxidation metabolism measurement in mammalian cells and tissues by quantitative LC/MS method (III)

Project description:Anti-oxidative metabolism measurement in mouse CSF by quantitative LC/MS method of mouse CSF at 24H of MTX treatment, for either control GFP or SOD3-overexpressing ChP mice.

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Anti-oxidative metabolism measurement in mammalian cells and tissues by quantitative LC/MS method (I)

Project description:Anti-oxidative metabolism measurement in CSF of mice by quantitative LC/MS method to analyze effect of MTX on level of antioxidants in mouse controls 0-48hrs in CSF and hippocampus.

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Anti-oxidative metabolism measurement in mammalian cells and tissues by quantitative LC/MS method (II)

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Highly multiplexed single-cell quantitative PCR

Project description:We present a microfluidic device for rapid gene expression profiling in single cells using multiplexed quantitative polymerase chain reaction (qPCR). This device integrates all processing steps, including cell isolation and lysis, complementary DNA synthesis, pre-amplification, sample splitting, and measurement in twenty separate qPCR reactions. Each of these steps is performed in parallel on up to 200 single cells per run. Experiments performed on dilutions of purified RNA establish assay linearity over a dynamic range of at least 104, a qPCR precision of 15 %, and detection sensitivity down to a single cDNA molecule. We demonstrate the application of our device for rapid profiling of microRNA expression in single cells. Measurements performed on a panel of twenty miRNA in two types of cells revealed clear cell-to-cell heterogeneity, with evidence of spontaneous differentiation manifest as distinct expression signatures. Highly multiplexed microfluidic RT-qPCR fills a gap in current capabilities for single-cell analysis, providing a rapid and cost-effective approach for profiling panels of marker genes, thereby complementing single-cell genomics methods that are best suited for global analysis and discovery. We expect this approach to enable new studies requiring fast, cost-effective, and precise measurements across hundreds of single cells.

2018-01-31 | GSE102734 | GEO

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