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Single-Cell Tagged Reverse Transcription (STRT-Seq)

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1979)

Abstract

Single-cell RNA sequencing (scRNA-seq) has become an established approach to profile entire transcriptomes of individual cells from different cell types, tissues, species, and organisms. Single-cell tagged reverse transcription sequencing (STRT-seq) is one of the early single-cell methods which utilize 5′ tag counting of transcripts. STRT-seq performed on microfluidics Fluidigm C1 platform (STRT-C1) is a flexible scRNA-seq approach that allows for accurate, sensitive and importantly molecular counting of transcripts at single-cell level. Herein, I describe the STRT-C1 method and the steps involved in capturing 96 cells across C1 microfluidics chip, cDNA synthesis, and preparing single-cell libraries for Illumina short-read sequencing.

Key words

STRT-C1 scRNA-seq 5′ Tag counting UMIs Single-cell tagged reverse transcription Fluidigm C1 Microfluidics 

Supplementary material

455552_1_En_9_MOESM1_ESM.docx (98 kb)
Supplementary Table 1 Barcodes and oligonucleotides sequences for STRT-seq (DOCX 34 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Functional Genomics and Metabolism Unit, Danish Institute of Advanced Study (D-IAS)University of Southern DenmarkOdenseDenmark

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