Using Fluidigm C1 to Generate Single-Cell Full-Length cDNA Libraries for mRNA Sequencing
Single-cell RNA sequencing has evolved into a benchmark application to study cellular heterogeneity, advancing our understanding of cellular differentiation, disease progression, and gene regulation in a multitude of research areas. The generation of high-quality cDNA, an important step in the experimental workflow when generating sequence-ready libraries, is critical to maximizing data quality. Here we describe a strategy that uses a microfluidic device (i.e., the C1™ IFC) to synthesize full-length cDNA from single cells in a fully automated, nanoliter-scale format. The device also facilitates confirmation of the presence of a single, viable cell and recording of phenotypic information, quality control measures that are crucial for streamlining downstream data processing and enhancing overall data validity.
Key wordsSingle-cell RNA-seq Gene expression profiling Full-length cDNA Single-cell transcriptomics Cell characterization
- 2.Kolodziejczyk AA, Kim JK, Tsang JC, Ilicic T, Henriksson J, Natarajan KN, Tuck AC, Gao X, Buhler M, Liu P, Marioni JC, Teichmann SA (2015) Single cell RNA-sequencing of pluripotent states unlocks modular transcriptional variation. Cell Stem Cell 17(4):471–485. https://doi.org/10.1016/j.stem.2015.09.011 CrossRefPubMedPubMedCentralGoogle Scholar
- 3.Zeisel A, Munoz-Manchado AB, Codeluppi S, Lonnerberg P, La Manno G, Jureus A, Marques S, Munguba H, He L, Betsholtz C, Rolny C, Castelo-Branco G, Hjerling-Leffler J, Linnarsson S (2015) Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science 347(6226):1138–1142. https://doi.org/10.1126/science.aaa1934 CrossRefPubMedGoogle Scholar
- 6.Baker SC, Bauer SR, Beyer RP, Brenton JD, Bromley B, Burrill J, Causton H, Conley MP, Elespuru R, Fero M, Foy C, Fuscoe J, Gao X, Gerhold DL, Gilles P, Goodsaid F, Guo X, Hackett J, Hockett RD, Ikonomi P, Irizarry RA, Kawasaki ES, Kaysser-Kranich T, Kerr K, Kiser G, Koch WH, Lee KY, Liu C, Liu ZL, Lucas A, Manohar CF, Miyada G, Modrusan Z, Parkes H, Puri RK, Reid L, Ryder TB, Salit M, Samaha RR, Scherf U, Sendera TJ, Setterquist RA, Shi L, Shippy R, Soriano JV, Wagar EA, Warrington JA, Williams M, Wilmer F, Wilson M, Wolber PK, Wu X, Zadro R, External RNACC (2005) The external RNA controls consortium: a progress report. Nat Methods 2(10):731–734. https://doi.org/10.1038/nmeth1005-731 CrossRefPubMedGoogle Scholar