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- Henriksson, Johan; Chen, Xi; Gomes, Tomás; Ullah, Ubaid; Meyer, Kerstin B.; Miragaia, Ricardo; Duddy, Graham; Pramanik, Jhuma; Yusa, Kosuke; Lahesmaa, Riitta; Teichmann, Sarah A.
- Cell 2019 v.176 no.4 pp. 882-896.e18
- CD4-positive T-lymphocytes; adaptive immunity; autoimmunity; cytokines; gene editing; genes; mammals; neoplasms; peroxisome proliferator-activated receptor gamma; sequence analysis
- ... T helper type 2 (Th2) cells are important regulators of mammalian adaptive immunity and have relevance for infection, autoimmunity, and tumor immunology. Using a newly developed, genome-wide retroviral CRISPR knockout (KO) library, combined with RNA-seq, ATAC-seq, and ChIP-seq, we have dissected the regulatory circuitry governing activation and differentiation of these cells. Our experiments disti ...
- Schiebinger, Geoffrey; Shu, Jian; Tabaka, Marcin; Cleary, Brian; Subramanian, Vidya; Solomon, Aryeh; Gould, Joshua; Liu, Siyan; Lin, Stacie; Berube, Peter; Lee, Lia; Chen, Jenny; Brumbaugh, Justin; Rigollet, Philippe; Hochedlinger, Konrad; Jaenisch, Rudolf; Regev, Aviv; Lander, Eric S.
- Cell 2019 v.176 no.4 pp. 928-943.e22
- cytokines; gene expression; models; sequence analysis; transcription factors
- ... Understanding the molecular programs that guide differentiation during development is a major challenge. Here, we introduce Waddington-OT, an approach for studying developmental time courses to infer ancestor-descendant fates and model the regulatory programs that underlie them. We apply the method to reconstruct the landscape of reprogramming from 315,000 single-cell RNA sequencing (scRNA-seq) pr ...