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26.06.18 New method for sequencing cell type-specific transcriptomes without cell sorting

last modified Jul 12, 2018 05:00 PM
In this Development report, Matsushima et al. present their new technique based on using a cell-specific promoter for in vivo metabolic RNA sequencing without cell sorting or RNA isolation
26.06.18 New method for sequencing cell type-specific transcriptomes without cell sorting

Schematic of new method

SLAM-ITseq: Sequencing cell type-specific transcriptomes without cell sorting

Matsushima W et al. (2018) Development .

 

Abstract from the paper

Cell type-specific transcriptome analysis is an essential tool in understanding biological processes in which diverse types of cells are involved. Although cell isolation methods such as fluorescence-activated cell sorting (FACS) in combination with transcriptome analysis have widely been used so far, their time-consuming and harsh procedures limit their applications.

Here, we report a novel in vivo metabolic RNA sequencing method, SLAM-ITseq, which metabolically labels RNA with 4-thiouracil in a specific cell type in vivo followed by detection through an RNA-seq-based method that specifically distinguishes the thiolated uridine by base conversion.

This method has successfully identified the cell type-specific transcriptome in three different tissues: endothelial cells in brain, epithelial cells in intestine, and adipocytes in white adipose tissue. Since this method does not require isolation of cells or RNA prior to the transcriptomic analysis, SLAM-ITseq provides an easy yet accurate snapshot of the transcriptional state in vivo.

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There is also a research highlight article in Development about the paper.

Read more about research in the Miska lab.

Watch Eric Miska describe his research in this short video.

Studying development to understand disease

The Gurdon Institute is funded by Wellcome and Cancer Research UK to study the biology of development, and how normal growth and maintenance go wrong in cancer and other diseases.

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