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Optimized single-nucleus transcriptional profiling by combinatorial indexing.
Martin BK, Qiu C, Nichols E, Phung M, Green-Gladden R, Srivatsan S, Blecher-Gonen R, Beliveau BJ, Trapnell C, Cao J, Shendure J. Martin BK, et al. Nat Protoc. 2023 Jan;18(1):188-207. doi: 10.1038/s41596-022-00752-0. Epub 2022 Oct 19. Nat Protoc. 2023. PMID: 36261634 Free PMC article. Review.
Embryo-scale, single-cell spatial transcriptomics.
Srivatsan SR, Regier MC, Barkan E, Franks JM, Packer JS, Grosjean P, Duran M, Saxton S, Ladd JJ, Spielmann M, Lois C, Lampe PD, Shendure J, Stevens KR, Trapnell C. Srivatsan SR, et al. Science. 2021 Jul 2;373(6550):111-117. doi: 10.1126/science.abb9536. Science. 2021. PMID: 34210887 Free PMC article.
Embryo model completes gastrulation to neurulation and organogenesis.
Amadei G, Handford CE, Qiu C, De Jonghe J, Greenfeld H, Tran M, Martin BK, Chen DY, Aguilera-Castrejon A, Hanna JH, Elowitz MB, Hollfelder F, Shendure J, Glover DM, Zernicka-Goetz M. Amadei G, et al. Nature. 2022 Oct;610(7930):143-153. doi: 10.1038/s41586-022-05246-3. Epub 2022 Aug 25. Nature. 2022. PMID: 36007540 Free PMC article.
Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.
Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S. Dekker J, et al. Mol Cell. 2023 Aug 3;83(15):2624-2640. doi: 10.1016/j.molcel.2023.06.018. Epub 2023 Jul 6. Mol Cell. 2023. PMID: 37419111 Free PMC article. Review.
Systematic reconstruction of cellular trajectories across mouse embryogenesis.
Qiu C, Cao J, Martin BK, Li T, Welsh IC, Srivatsan S, Huang X, Calderon D, Noble WS, Disteche CM, Murray SA, Spielmann M, Moens CB, Trapnell C, Shendure J. Qiu C, et al. Nat Genet. 2022 Mar;54(3):328-341. doi: 10.1038/s41588-022-01018-x. Epub 2022 Mar 14. Nat Genet. 2022. PMID: 35288709 Free PMC article.
A single-cell time-lapse of mouse prenatal development from gastrula to birth.
Qiu C, Martin BK, Welsh IC, Daza RM, Le TM, Huang X, Nichols EK, Taylor ML, Fulton O, O'Day DR, Gomes AR, Ilcisin S, Srivatsan S, Deng X, Disteche CM, Noble WS, Hamazaki N, Moens CB, Kimelman D, Cao J, Schier AF, Spielmann M, Murray SA, Trapnell C, Shendure J. Qiu C, et al. Nature. 2024 Feb;626(8001):1084-1093. doi: 10.1038/s41586-024-07069-w. Epub 2024 Feb 14. Nature. 2024. PMID: 38355799 Free PMC article.
Targeted DNase Hi-C.
Duan Z. Duan Z. Methods Mol Biol. 2021;2157:65-83. doi: 10.1007/978-1-0716-0664-3_5. Methods Mol Biol. 2021. PMID: 32820399 Free PMC article.
Symbolic recording of signalling and cis-regulatory element activity to DNA.
Chen W, Choi J, Li X, Nathans JF, Martin B, Yang W, Hamazaki N, Qiu C, Lalanne JB, Regalado S, Kim H, Agarwal V, Nichols E, Leith A, Lee C, Shendure J. Chen W, et al. Nature. 2024 Aug;632(8027):1073-1081. doi: 10.1038/s41586-024-07706-4. Epub 2024 Jul 17. Nature. 2024. PMID: 39020177 Free PMC article.
Retinoic acid induces human gastruloids with posterior embryo-like structures.
Hamazaki N, Yang W, Kubo CA, Qiu C, Martin BK, Garge RK, Regalado SG, Nichols EK, Pendyala S, Bradley N, Fowler DM, Lee C, Daza RM, Srivatsan S, Shendure J. Hamazaki N, et al. Nat Cell Biol. 2024 Oct;26(10):1790-1803. doi: 10.1038/s41556-024-01487-8. Epub 2024 Aug 20. Nat Cell Biol. 2024. PMID: 39164488 Free PMC article.
37 results