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Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

ABSTRACT: We assessed Smart-Seq, a new single-cell RNA-Seq library preparation method, on a variety of mouse and human RNA samples or cells.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE38495 | GEO | 2012/07/22

SECONDARY ACCESSION(S): PRJNA170814

REPOSITORIES: GEO

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Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

Project description:We assessed Smart-Seq, a new single-cell RNA-Seq library preparation method, on a variety of mouse and human RNA samples or cells. We generated RNA-Seq libraries for dilution series of MAQC reference RNA and mouse brain RNA to assess technical reproducibility, and for a variety of individual cells including putative circulating tumour cells.

2012-07-22 | E-GEOD-38495 | biostudies-arrayexpress

Full-length mRNA sequencing reveals principles of poly(A) tail length control

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Project description:Here we present a performance evaluation of three different plate-based scRNA-seq protocols. Two commercially available kits; NEBNext Single Cell/ Low Input RNA Library Prep Kit (NEB), SMART-seq HT kit (Takara), and non-commercially available protocol Genome & transcriptome sequencing (G&T). We evaluated each kit based upon sensitivity, reproducibility, ease of use and price point per cell. This evaluation is specifically relevant for implementation of scRNA-seq in e.g. diagnostics, requiring high sensitivity in regards of gene detection, high reproducibility between samples, minimum hands on time and smooth sample preparation for technicians, as well as keeping a reasonable price point per patient. G&T protocol delivered the highest detection of genes per single cell, at the absolute lowest price point. Takara's kit delivered likewise high gene detection per single cell, and high reproducibility between sample, however at the absolute highest price points. Here we present pros and cons of each protocol, sequencing breast cancer cell line T47D.

2020-08-01 | GSE155506 | GEO

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

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Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells.

Project description:Genome-wide transcriptome analyses are routinely used to monitor tissue-, disease- and cell type–specific gene expression, but it has been technically challenging to generate expression profiles from single cells. Here we describe a robust mRNA-Seq protocol (Smart-Seq) that is applicable down to single cell levels. Compared with existing methods, Smart-Seq has improved read coverage across transcripts, which enhances detailed analyses of alternative transcript isoforms and identification of single-nucleotide polymorphisms. We determined the sensitivity and quantitative accuracy of Smart-Seq for single-cell transcriptomics by evaluating it on total RNA dilution series. We found that although gene expression estimates from single cells have increased noise, hundreds of differentially expressed genes could be identified using few cells per cell type. Applying Smart-Seq to circulating tumor cells from melanomas, we identified distinct gene expression patterns, including candidate biomarkers for melanoma circulating tumor cells. Our protocol will be useful for addressing fundamental biological problems requiring genome-wide transcriptome profiling in rare cells.

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Improved Smart-Seq for sensitive full-length transcriptome profiling in single cells

Project description:Improved Smart-Seq for sensitive full-length transcriptome profiling in single cells. Cells of four different origins were profiled using commercial SMARTer and compared to five variants of an improved protocol (Smart-Seq2).

2013-09-01 | E-GEOD-49321 | biostudies-arrayexpress

Improved Smart-Seq for sensitive full-length transcriptome profiling in single cells

Project description:Improved Smart-Seq for sensitive full-length transcriptome profiling in single cells.

2013-09-01 | GSE49321 | GEO

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CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing

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Increased circulating full-length betatrophin levels in drug-naive metabolic syndrome.

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