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SMARTer single cell total RNA sequencing

ABSTRACT: SMARTer single cell total RNA sequencing

PROVIDER: PRJNA490894 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7826630.fastq.gz	Fastqsanger.gz
	SRR7826640.fastq.gz	Fastqsanger.gz
	SRR7826650.fastq.gz	Fastqsanger.gz
	SRR7826660.fastq.gz	Fastqsanger.gz
	SRR7826670.fastq.gz	Fastqsanger.gz

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Project description:Single cell RNA sequencing methods have been increasingly used to understand cellular heterogeneity. Nevertheless, most of these methods suffer from one or more limitations, such as focusing only on polyadenylated RNA, sequencing of only the 3' end of the transcript, an exuberant fraction of reads mapping to ribosomal RNA, and the unstranded nature of the sequencing data. Here, we developed a novel single cell strand-specific total RNA library preparation method addressing all the aforementioned shortcomings. Our method was validated on a microfluidics system using three different cancer cell lines undergoing a chemical or genetic perturbation and on two other cancer cell lines sorted in microplates. We demonstrate that our total RNA-seq method detects an equal or higher number of genes compared to classic polyA[+] RNA-seq, including novel and non-polyadenylated genes. The obtained RNA expression patterns also recapitulate the expected biological signal. Inherent to total RNA-seq, our method is also able to detect circular RNAs. Taken together, SMARTer single cell total RNA sequencing is very well suited for any single cell sequencing experiment in which transcript level information is needed beyond polyadenylated genes.

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SMARTer single cell total RNA sequencing [NGP]

Project description:single cell polyA+ and total RNA-seq data was generated for NGP, SK-N-BE-2C and SHSY5Y-MYCN-TR cells

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SMARTer single cell total RNA sequencing [SHSY5Y-MYCN-TR]

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Single cell RNA-sequencing of Spike-ins and mESC using SMARTer on C1 System

Project description:In this study, we assess technical differences between commonly used single-cell RNA-Sequencing (scRNA-Seq) methods. We perform scRNA-seq on a homogenous population of mouse embryonic stem cells along with two kinds of control spike-in molecules to assess sensitivity and accuracy of these specific methods. In this dataset, we perform SMARTer method on Fluidigm C1 system and generate single-cell libraries using Nextera XT kit

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