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CROPseq-Guide-Puro Citations (33)

Originally described in: Pooled CRISPR screening with single-cell transcriptome readout.
Datlinger P, Rendeiro AF, Schmidl C, Krausgruber T, Traxler P, Klughammer J, Schuster LC, Kuchler A, Alpar D, Bock C Nat Methods. 2017 Jan 18. doi: 10.1038/nmeth.4177. PubMed Journal

Articles Citing CROPseq-Guide-Puro

Articles
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

Associated Plasmids
Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function. Shifrut E, Carnevale J, Tobin V, Roth TL, Woo JM, Bui CT, Li PJ, Diolaiti ME, Ashworth A, Marson A. Cell. 2018 Dec 13;175(7):1958-1971.e15. doi: 10.1016/j.cell.2018.10.024. Epub 2018 Nov 15. PubMed
Experimental and Computational Approaches for Single-Cell Enhancer Perturbation Assay. Xie S, Hon GC. Methods Mol Biol. 2019;1935:203-221. doi: 10.1007/978-1-4939-9057-3_14. PubMed
Single-Cell RNA-Sequencing-Based CRISPRi Screening Resolves Molecular Drivers of Early Human Endoderm Development. Genga RMJ, Kernfeld EM, Parsi KM, Parsons TJ, Ziller MJ, Maehr R. Cell Rep. 2019 Apr 16;27(3):708-718.e10. doi: 10.1016/j.celrep.2019.03.076. PubMed

Associated Plasmids
CRISPR Screening in Single Cells. Henriksson J. Methods Mol Biol. 2019;1979:395-406. doi: 10.1007/978-1-4939-9240-9_23. PubMed
CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons. Tian R, Gachechiladze MA, Ludwig CH, Laurie MT, Hong JY, Nathaniel D, Prabhu AV, Fernandopulle MS, Patel R, Abshari M, Ward ME, Kampmann M. Neuron. 2019 Aug 5. pii: S0896-6273(19)30640-3. doi: 10.1016/j.neuron.2019.07.014. PubMed

Associated Plasmids
Genome-scale CRISPR screens are efficient in non-homologous end-joining deficient cells. Ferreira da Silva J, Salic S, Wiedner M, Datlinger P, Essletzbichler P, Hanzl A, Superti-Furga G, Bock C, Winter G, Loizou JI. Sci Rep. 2019 Oct 31;9(1):15751. doi: 10.1038/s41598-019-52078-9. PubMed
Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules. Xie S, Armendariz D, Zhou P, Duan J, Hon GC. Cell Rep. 2019 Nov 26;29(9):2570-2578.e5. doi: 10.1016/j.celrep.2019.10.073. PubMed
Single-cell analysis of a mutant library generated using CRISPR-guided deaminase in human melanoma cells. Jun S, Lim H, Chun H, Lee JH, Bang D. Commun Biol. 2020 Apr 2;3(1):154. doi: 10.1038/s42003-020-0888-2. PubMed
Targeted Perturb-seq enables genome-scale genetic screens in single cells. Schraivogel D, Gschwind AR, Milbank JH, Leonce DR, Jakob P, Mathur L, Korbel JO, Merten CA, Velten L, Steinmetz LM. Nat Methods. 2020 Jun;17(6):629-635. doi: 10.1038/s41592-020-0837-5. Epub 2020 Jun 1. PubMed
High-performance CRISPR-Cas12a genome editing for combinatorial genetic screening. Gier RA, Budinich KA, Evitt NH, Cao Z, Freilich ES, Chen Q, Qi J, Lan Y, Kohli RM, Shi J. Nat Commun. 2020 Jul 13;11(1):3455. doi: 10.1038/s41467-020-17209-1. PubMed

Associated Plasmids
Cell-type-specific 3D epigenomes in the developing human cortex. Song M, Pebworth MP, Yang X, Abnousi A, Fan C, Wen J, Rosen JD, Choudhary MNK, Cui X, Jones IR, Bergenholtz S, Eze UC, Juric I, Li B, Maliskova L, Lee J, Liu W, Pollen AA, Li Y, Wang T, Hu M, Kriegstein AR, Shen Y. Nature. 2020 Nov;587(7835):644-649. doi: 10.1038/s41586-020-2825-4. Epub 2020 Oct 14. PubMed
Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens. Papalexi E, Mimitou EP, Butler AW, Foster S, Bracken B, Mauck WM 3rd, Wessels HH, Hao Y, Yeung BZ, Smibert P, Satija R. Nat Genet. 2021 Mar;53(3):322-331. doi: 10.1038/s41588-021-00778-2. Epub 2021 Mar 1. PubMed
Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens. Liscovitch-Brauer N, Montalbano A, Deng J, Mendez-Mancilla A, Wessels HH, Moss NG, Kung CY, Sookdeo A, Guo X, Geller E, Jaini S, Smibert P, Sanjana NE. Nat Biotechnol. 2021 Apr 29. pii: 10.1038/s41587-021-00902-x. doi: 10.1038/s41587-021-00902-x. PubMed

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Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing. Datlinger P, Rendeiro AF, Boenke T, Senekowitsch M, Krausgruber T, Barreca D, Bock C. Nat Methods. 2021 Jun;18(6):635-642. doi: 10.1038/s41592-021-01153-z. Epub 2021 May 31. PubMed
Pooled genetic perturbation screens with image-based phenotypes. Feldman D, Funk L, Le A, Carlson RJ, Leiken MD, Tsai F, Soong B, Singh A, Blainey PC. Nat Protoc. 2022 Feb;17(2):476-512. doi: 10.1038/s41596-021-00653-8. Epub 2022 Jan 12. PubMed
CRISPR activation and interference screens decode stimulation responses in primary human T cells. Schmidt R, Steinhart Z, Layeghi M, Freimer JW, Bueno R, Nguyen VQ, Blaeschke F, Ye CJ, Marson A. Science. 2022 Feb 4;375(6580):eabj4008. doi: 10.1126/science.abj4008. Epub 2022 Feb 4. PubMed

Associated Plasmids
Computational identification of clonal cells in single-cell CRISPR screens. Wang Y, Xie S, Armendariz D, Hon GC. BMC Genomics. 2022 Feb 15;23(1):135. doi: 10.1186/s12864-022-08359-1. PubMed
A time-resolved, multi-symbol molecular recorder via sequential genome editing. Choi J, Chen W, Minkina A, Chardon FM, Suiter CC, Regalado SG, Domcke S, Hamazaki N, Lee C, Martin B, Daza RM, Shendure J. Nature. 2022 Jul 6. pii: 10.1038/s41586-022-04922-8. doi: 10.1038/s41586-022-04922-8. PubMed

Associated Plasmids
Runx2 regulates chromatin accessibility to direct the osteoblast program at neonatal stages. Hojo H, Saito T, He X, Guo Q, Onodera S, Azuma T, Koebis M, Nakao K, Aiba A, Seki M, Suzuki Y, Okada H, Tanaka S, Chung UI, McMahon AP, Ohba S. Cell Rep. 2022 Sep 6;40(10):111315. doi: 10.1016/j.celrep.2022.111315. PubMed
Single-cell CRISPR immune screens reveal immunological roles of tumor intrinsic factors. Hou J, Liang S, Xu C, Wei Y, Wang Y, Tan Y, Sahni N, McGrail DJ, Bernatchez C, Davies M, Li Y, Chen R, Yi SS, Chen Y, Yee C, Chen K, Peng W. NAR Cancer. 2022 Dec 9;4(4):zcac038. doi: 10.1093/narcan/zcac038. eCollection 2022 Dec. PubMed
High-content image-based CRISPR screening reveals regulators of 3D genome architectures. Hu M, Yang B, Jensen TB, Radda JSD, Cheng Y, Jin S, Wang S. bioRxiv. 2023 Feb 1:2023.01.31.525983. doi: 10.1101/2023.01.31.525983. Preprint. PubMed
Engineered MED12 mutations drive uterine fibroid-like transcriptional and metabolic programs by altering the 3D genome compartmentalization. Buyukcelebi K, Chen X, Abdula F, Duval A, Ozturk H, Seker-Polat F, Jin Q, Yin P, Feng Y, Wei JJ, Bulun S, Yue F, Adli M. Res Sq. 2023 Feb 9:rs.3.rs-2537075. doi: 10.21203/rs.3.rs-2537075/v1. Preprint. PubMed
CRISPR screens identify gene targets at breast cancer risk loci. Tuano NK, Beesley J, Manning M, Shi W, Perlaza-Jimenez L, Malaver-Ortega LF, Paynter JM, Black D, Civitarese A, McCue K, Hatzipantelis A, Hillman K, Kaufmann S, Sivakumaran H, Polo JM, Reddel RR, Band V, French JD, Edwards SL, Powell DR, Chenevix-Trench G, Rosenbluh J. Genome Biol. 2023 Mar 29;24(1):59. doi: 10.1186/s13059-023-02898-w. PubMed

Associated Plasmids
CHD-associated enhancers shape human cardiomyocyte lineage commitment. Armendariz DA, Goetsch SC, Sundarrajan A, Sivakumar S, Wang Y, Xie S, Munshi NV, Hon GC. Elife. 2023 Apr 25;12:e86206. doi: 10.7554/eLife.86206. PubMed
Engineered MED12 mutations drive leiomyoma-like transcriptional and metabolic programs by altering the 3D genome compartmentalization. Buyukcelebi K, Chen X, Abdula F, Elkafas H, Duval AJ, Ozturk H, Seker-Polat F, Jin Q, Yin P, Feng Y, Bulun SE, Wei JJ, Yue F, Adli M. Nat Commun. 2023 Jul 10;14(1):4057. doi: 10.1038/s41467-023-39684-y. PubMed
GiRAFR improves gRNA detection and annotation in single-cell CRISPR screens. Yu Q, Van Minsel P, Galle E, Thienpont B. Commun Biol. 2023 Sep 23;6(1):975. doi: 10.1038/s42003-023-05351-7. PubMed
In-organoid single-cell CRISPR screening reveals determinants of hepatocyte differentiation and maturation. Liang J, Wei J, Cao J, Qian J, Gao R, Li X, Wang D, Gu Y, Dong L, Yu J, Zhao B, Wang X. Genome Biol. 2023 Oct 31;24(1):251. doi: 10.1186/s13059-023-03084-8. PubMed
Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes. Wang Y, Armendariz D, Wang L, Zhao H, Xie S, Hon GC. bioRxiv [Preprint]. 2023 Nov 20:2023.11.20.567880. doi: 10.1101/2023.11.20.567880. PubMed
Single cell multi-omics reveal intra-cell-line heterogeneity across human cancer cell lines. Zhu Q, Zhao X, Zhang Y, Li Y, Liu S, Han J, Sun Z, Wang C, Deng D, Wang S, Tang Y, Huang Y, Jiang S, Tian C, Chen X, Yuan Y, Li Z, Yang T, Lai T, Liu Y, Yang W, Zou X, Zhang M, Cui H, Liu C, Jin X, Hu Y, Chen A, Xu X, Li G, Hou Y, Liu L, Liu S, Fang L, Chen W, Wu L. Nat Commun. 2023 Dec 9;14(1):8170. doi: 10.1038/s41467-023-43991-9. PubMed
High throughput functional profiling of genes at intraocular pressure loci reveals distinct networks for glaucoma. Greatbatch CJ, Lu Q, Hung S, Barnett AJ, Wing K, Liang H, Han X, Zhou T, Siggs OM, Mackey DA, Cook AL, Senabouth A, Liu GS, Craig JE, MacGregor S, Powell JE, Hewitt AW. Hum Mol Genet. 2024 Apr 18;33(9):739-751. doi: 10.1093/hmg/ddae003. PubMed
Detecting subtle transcriptomic perturbations induced by lncRNAs knock-down in single-cell CRISPRi screening using a new sparse supervised autoencoder neural network. Truchi M, Lacoux C, Gille C, Fassy J, Magnone V, Lopes Goncalves R, Girard-Riboulleau C, Manosalva-Pena I, Gautier-Isola M, Lebrigand K, Barbry P, Spicuglia S, Vassaux G, Rezzonico R, Barlaud M, Mari B. Front Bioinform. 2024 Mar 4;4:1340339. doi: 10.3389/fbinf.2024.1340339. eCollection 2024. PubMed
Pooled multicolour tagging for visualizing subcellular protein dynamics. Reicher A, Reinis J, Ciobanu M, Ruzicka P, Malik M, Siklos M, Kartysh V, Tomek T, Koren A, Rendeiro AF, Kubicek S. Nat Cell Biol. 2024 May;26(5):745-756. doi: 10.1038/s41556-024-01407-w. Epub 2024 Apr 19. PubMed

Associated Plasmids

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