Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.
Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.
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DOI：
10.1016/j.cell.2016.11.038
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发表时间：
2016-12-15
期刊：
影响因子：
64.5
通讯作者：
Regev, Aviv
中科院分区：
文献类型：
--
作者：
Dixit, Atray;Pamas, Oren;Li, Biyu;Chen, Jenny;Fulco, Charles P.;Jerby-Amon, Livnat;Marjanovic, Nemanja D.;Dionne, Danielle;Burks, Tyler;Raychowdhury, Raktima;Adamson, Britt;Norman, Thomas M.;Lander, Eric S.;Weissman, Jonathan S.;Friedman, Nir;Regev, Aviv
基因筛查有助于推断哺乳动物细胞的基因功能，但在规模上分析复杂的表型--如转录图谱--仍然是困难的。在这里，我们开发了扰动SEQ，将单细胞RNA-SEQ和基于CRISPR的扰动相结合，在一个池中执行许多这样的分析。我们通过分析免疫细胞和细胞系中的200,000个细胞，重点研究调节树突状细胞对脂多糖(LPS)反应的转录因子，展示了扰动序列。Perturb-seq可准确识别受个体扰动及其遗传相互作用影响的单个基因靶点、基因签名和细胞状态。我们假定在免疫激活过程中，分化调节、抗病毒反应和线粒体功能具有新的功能。通过将许多高含量的测量分解为扰动、它们的相互作用和不同的细胞元数据的影响，perturb-seq极大地扩大了集合基因组分析的范围。
Genetic screens help infer gene function in mammalian cells, but it has remained difficult to assay complex phenotypes – such as transcriptional profiles – at scale. Here, we develop Perturb-seq, combining single cell RNA-seq and CRISPR based perturbations to perform many such assays in a pool. We demonstrate Perturb-seq by analyzing 200,000 cells in immune cells and cell lines, focusing on transcription factors regulating the response of dendritic cells to lipopolysaccharide (LPS). Perturb-seq accurately identifies individual gene targets, gene signatures, and cell states affected by individual perturbations and their genetic interactions. We posit new functions for regulators of differentiation, the anti-viral response, and mitochondrial function during immune activation. By decomposing many high content measurements into the effects of perturbations, their interactions, and diverse cell metadata, Perturb-seq dramatically increases the scope of pooled genomic assays.
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影响因子：
50.3
作者：
Berger AH;Brooks AN;Wu X;Shrestha Y;Chouinard C;Piccioni F;Bagul M;Kamburov A;Imielinski M;Hogstrom L;Zhu C;Yang X;Pantel S;Sakai R;Watson J;Kaplan N;Campbell JD;Singh S;Root DE;Narayan R;Natoli T;Lahr DL;Tirosh I;Tamayo P;Getz G;Wong B;Doench J;Subramanian A;Golub TR;Meyerson M;Boehm JS
通讯作者：
Boehm JS
DOI：
10.1126/science.1179050
发表时间：
2009-10-09
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Amit I;Garber M;Chevrier N;Leite AP;Donner Y;Eisenhaure T;Guttman M;Grenier JK;Li W;Zuk O;Schubert LA;Birditt B;Shay T;Goren A;Zhang X;Smith Z;Deering R;McDonald RC;Cabili M;Bernstein BE;Rinn JL;Meissner A;Root DE;Hacohen N;Regev A
通讯作者：
Regev A
影响因子：
64.5
作者：
Chevrier N;Mertins P;Artyomov MN;Shalek AK;Iannacone M;Ciaccio MF;Gat-Viks I;Tonti E;DeGrace MM;Clauser KR;Garber M;Eisenhaure TM;Yosef N;Robinson J;Sutton A;Andersen MS;Root DE;von Andrian U;Jones RB;Park H;Carr SA;Regev A;Amit I;Hacohen N
通讯作者：
Hacohen N
CRISPR-CAS9介导的基因失活的高度活性SGRNA的合理设计。
影响因子：
46.9
作者：
Doench, John G.;Hartenian, Ella;Graham, Daniel B.;Tothova, Zuzana;Hegde, Mudra;Smith, Ian;Sullender, Meagan;Ebert, Benjamin L.;Xavier, Ramnik J.;Root, David E.
通讯作者：
Root, David E.
影响因子：
25.7
作者：
Elsharkawy, Ahmed M.;Oakley, Fiona;Lin, Feng;Packham, Graham;Mann, Derek A.;Mann, Jelena
通讯作者：
Mann, Jelena