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Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies

Travis K.Hughes, Marc H.Wadsworth II, Todd M.Gierahn, Tran Do, David Weiss, Priscila R.Andrade, Feiyang Ma, Bruno J.de Andrade Silva, Shuai Shao, Lam C.Tsoi, Jose Ordovas-Montanes, Johann E.Gudjonsson, Robert L.Modlin, J. Christopher Love, Alex K.Shalek

High-throughput single-cell RNA-sequencing (scRNA-seq) methodologies enable characterization of complex biological samples by increasing the number of cells that can be profiled contemporaneously. Nevertheless, these approaches recover less information per cell than low-throughput strategies. To accurately report the expression of key phenotypic features of cells, scRNA-seq platforms are needed that are both high fidelity and high throughput. To address this need, we created Seq-Well S3 (<e2><80><98><e2><80><98>Second-Strand Synthesis<e2><80><99><e2><80><99>), a massively parallel scRNA-seq protocol that uses a randomly primed second-strand synthesis to recover complementary DNA (cDNA) molecules that were successfully reverse transcribed but to which a second oligonucleotide handle, necessary for subsequent whole transcriptome amplification, was not appended due to inefficient template switching. Seq-Well S3 increased the efficiency of transcript capture and gene detection compared with that of previous iterations by up to 10- and 5-fold, respectively. We used SeqWell S3 to chart the transcriptional landscape of five human inflammatory skin diseases, thus providing a resource for the further study of human skin inflammation.

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Species: human
Number of cells: 38274
Number of downloads: 26
Study size: 954MB
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Seq-Well S3