CROP-seq-opti Citations (13)

Originally described in: On the design of CRISPR-based single-cell molecular screens.
Hill AJ, McFaline-Figueroa JL, Starita LM, Gasperini MJ, Matreyek KA, Packer J, Jackson D, Shendure J, Trapnell C Nat Methods. 2018 Feb 19. pii: nmeth.4604. doi: 10.1038/nmeth.4604. PubMed Journal

---

Articles Citing CROP-seq-opti

Articles
A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Gasperini M, Hill AJ, McFaline-Figueroa JL, Martin B, Kim S, Zhang MD, Jackson D, Leith A, Schreiber J, Noble WS, Trapnell C, Ahituv N, Shendure J. Cell. 2019 Jan 10;176(1-2):377-390.e19. doi: 10.1016/j.cell.2018.11.029. Epub 2019 Jan 3. PubMed
CRISPR Screening in Single Cells. Henriksson J. Methods Mol Biol. 2019;1979:395-406. doi: 10.1007/978-1-4939-9240-9_23. PubMed
Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes. Song M, Yang X, Ren X, Maliskova L, Li B, Jones IR, Wang C, Jacob F, Wu K, Traglia M, Tam TW, Jamieson K, Lu SY, Ming GL, Li Y, Yao J, Weiss LA, Dixon JR, Judge LM, Conklin BR, Song H, Gan L, Shen Y. Nat Genet. 2019 Aug;51(8):1252-1262. doi: 10.1038/s41588-019-0472-1. Epub 2019 Jul 31. PubMed
An Embryonic Diapause-like Adaptation with Suppressed Myc Activity Enables Tumor Treatment Persistence. Dhimolea E, de Matos Simoes R, Kansara D, Al'Khafaji A, Bouyssou J, Weng X, Sharma S, Raja J, Awate P, Shirasaki R, Tang H, Glassner BJ, Liu Z, Gao D, Bryan J, Bender S, Roth J, Scheffer M, Jeselsohn R, Gray NS, Georgakoudi I, Vazquez F, Tsherniak A, Chen Y, Welm A, Duy C, Melnick A, Bartholdy B, Brown M, Culhane AC, Mitsiades CS. Cancer Cell. 2021 Feb 8;39(2):240-256.e11. doi: 10.1016/j.ccell.2020.12.002. Epub 2021 Jan 7. PubMed
Genome-wide enhancer maps link risk variants to disease genes. Nasser J, Bergman DT, Fulco CP, Guckelberger P, Doughty BR, Patwardhan TA, Jones TR, Nguyen TH, Ulirsch JC, Lekschas F, Mualim K, Natri HM, Weeks EM, Munson G, Kane M, Kang HY, Cui A, Ray JP, Eisenhaure TM, Collins RL, Dey K, Pfister H, Price AL, Epstein CB, Kundaje A, Xavier RJ, Daly MJ, Huang H, Finucane HK, Hacohen N, Lander ES, Engreitz JM. Nature. 2021 May;593(7858):238-243. doi: 10.1038/s41586-021-03446-x. Epub 2021 Apr 7. PubMed
Inducible CRISPR activation screen for interferon-stimulated genes identifies OAS1 as a SARS-CoV-2 restriction factor. Danziger O, Patel RS, DeGrace EJ, Rosen MR, Rosenberg BR. PLoS Pathog. 2022 Apr 14;18(4):e1010464. doi: 10.1371/journal.ppat.1010464. eCollection 2022 Apr. PubMed Associated Plasmids pHR-PGK- dCas9-SunTag-P2A-HygR pCW-tTRE-scFv-SunTag
Compressed Perturb-seq: highly efficient screens for regulatory circuits using random composite perturbations. Yao D, Binan L, Bezney J, Simonton B, Freedman J, Frangieh CJ, Dey K, Geiger-Schuller K, Eraslan B, Gusev A, Regev A, Cleary B. bioRxiv. 2023 Jan 23:2023.01.23.525200. doi: 10.1101/2023.01.23.525200. Preprint. PubMed
Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy. McFaline-Figueroa JL, Srivatsan S, Hill AJ, Gasperini M, Jackson DL, Saunders L, Domcke S, Regalado SG, Lazarchuck P, Alvarez S, Monnat RJ, Shendure J, Trapnell C. bioRxiv. 2023 Jun 14:2023.03.10.531983. doi: 10.1101/2023.03.10.531983. Preprint. PubMed
LRP8-mediated selenocysteine uptake is a targetable vulnerability in MYCN-amplified neuroblastoma. Alborzinia H, Chen Z, Yildiz U, Freitas FP, Vogel FCE, Varga JP, Batani J, Bartenhagen C, Schmitz W, Buchel G, Michalke B, Zheng J, Meierjohann S, Girardi E, Espinet E, Florez AF, Dos Santos AF, Aroua N, Cheytan T, Haenlin J, Schlicker L, Xavier da Silva TN, Przybylla A, Zeisberger P, Superti-Furga G, Eilers M, Conrad M, Fabiano M, Schweizer U, Fischer M, Schulze A, Trumpp A, Friedmann Angeli JP. EMBO Mol Med. 2023 Aug 7;15(8):e18014. doi: 10.15252/emmm.202318014. Epub 2023 Jul 12. PubMed
Functional characterization of Alzheimer's disease genetic variants in microglia. Yang X, Wen J, Yang H, Jones IR, Zhu X, Liu W, Li B, Clelland CD, Luo W, Wong MY, Ren X, Cui X, Song M, Liu H, Chen C, Eng N, Ravichandran M, Sun Y, Lee D, Van Buren E, Jiang MZ, Chan CSY, Ye CJ, Perera RM, Gan L, Li Y, Shen Y. Nat Genet. 2023 Oct;55(10):1735-1744. doi: 10.1038/s41588-023-01506-8. Epub 2023 Sep 21. PubMed Associated Plasmids CYLBL_Neo_CAGdCas9-KRAB
Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens. Xu Z, Sziraki A, Lee J, Zhou W, Cao J. Nat Biotechnol. 2023 Sep 25. doi: 10.1038/s41587-023-01948-9. PubMed
CRISPR-Cas and CRISPR-based screening system for precise gene editing and targeted cancer therapy. Qin M, Deng C, Wen L, Luo G, Meng Y. J Transl Med. 2024 May 30;22(1):516. doi: 10.1186/s12967-024-05235-2. PubMed
Defining cis-regulatory elements and transcription factors that control human cortical interneuron development. Chapman G, Determan J, Jetter H, Kaushik K, Prakasam R, Kroll KL. iScience. 2024 May 11;27(6):109967. doi: 10.1016/j.isci.2024.109967. eCollection 2024 Jun 21. PubMed

If you have published an article using this material, please email us at to have your article added to this page.