The lab has developed several microarray-based sequencing techniques for immune cell profiling. In collaboration with the Shalek lab, we developed Seq-Well, a cost effective scRNAseq platform designed to handle low sample inputs. We have also pioneered technologies on the profiling of T cell and B cell receptors. An example is B3E-seq – full-length BCR sequencing from 3’-barcoded libraries, which are typically insufficient for receptor sequencing. These efforts have led to the spinout of Honeycomb Bio and a dedicated core facility at the KI.
Relevant Publications
Morgan DM, Zhang YJ, Kim JH, Murillo M, Singh S, Loschko J, Surendran N, Sekulovic O, Feng E, Shi S, Irvine DJ, Patil SU, Kanevsky I, Chorro L, Christopher Love J. Full-length single-cell BCR sequencing paired with RNA sequencing reveals convergent responses to pneumococcal vaccination. Commun Biol. 2024 Sep 28;7(1):1208. doi: 10.1038/s42003-024-06823-0. PMID: 39341987; PMCID: PMC11438910.
Hughes TK, Wadsworth MH 2nd, Gierahn TM, Do T, Weiss D, Andrade PR, Ma F, de Andrade Silva BJ, Shao S, Tsoi LC, Ordovas-Montanes J, Gudjonsson JE, Modlin RL, Love JC, Shalek A. Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies. Immunity. 2020 Oct.13. doi: 10.1016/j.immuni.2020.09.015.
Tu AA, Gierahn TM, Monian B, Morgan DM, Mehta NK, Ruiter B, Shreffler WG, Shalek AK, Love JC. TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures. Nat Immunol. 2019 Dec;20(12):1692-1699. doi: 10.1038/s41590-019-0544-5.
Gierahn TM, Wadsworth MH 2nd, Hughes TK, Bryson BD, Butler A, Satija R, Fortune S, Love JC, Shalek AK. Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. Nat Methods. 2017 Feb 13. doi: 10.1038/nmeth.4179.