ENCoRE: an efficient software for CRISPR screens identifies new players in extrinsic apoptosis.
ENCoRE: an efficient software for CRISPR screens identifies new players in extrinsic apoptosis.
复制标题
DOI：
10.1186/s12864-017-4285-2
复制
发表时间：
2017-11-25
期刊：
影响因子：
4.4
通讯作者：
Schick JA
中科院分区：
文献类型：
--
作者：
Trümbach D;Pfeiffer S;Poppe M;Scherb H;Doll S;Wurst W;Schick JA
随着CRISPR/Cas9介导的在体细胞中使用汇集的指导文库的筛选变得越来越成熟，出现了对快速和准确的伴随信息学工具的未满足的需求。我们已经开发了一个轻量级和高效的软件，可以轻松地操作大型原始的下一代测序数据集，从这样的屏幕到信息的关系上下文与图形支持。名为ENCoRE（Easy NGS-to-Gene CRISPR Results）的软件的优点包括简单的图形工作流程，平台独立性，本地和快速多线程处理，数据预处理和自定义库导入的基因图谱。我们证明了ENCoRE在肿瘤坏死因子-α激发后询问合并CRISPR细胞活力筛选结果的能力。结果不仅确定了外在凋亡信号的刻板球员，但两个尚未表征的成员的外在凋亡级联，Smg 7和Ces 2a。我们进一步验证和表征了这些基因中含有突变的细胞系对一组细胞死亡刺激和参与p53信号传导的作用。总之，该软件使拥有敏感数据或无法访问信息核心的实验室科学家能够快速解释来自合并CRISPR/Cas9文库筛选的大规模实验结果。本文的在线版本（10.1186/s12864-017-4285-2）包含补充材料，可供授权用户使用。
As CRISPR/Cas9 mediated screens with pooled guide libraries in somatic cells become increasingly established, an unmet need for rapid and accurate companion informatics tools has emerged. We have developed a lightweight and efficient software to easily manipulate large raw next generation sequencing datasets derived from such screens into informative relational context with graphical support. The advantages of the software entitled ENCoRE (Easy NGS-to-Gene CRISPR REsults) include a simple graphical workflow, platform independence, local and fast multithreaded processing, data pre-processing and gene mapping with custom library import. We demonstrate the capabilities of ENCoRE to interrogate results from a pooled CRISPR cellular viability screen following Tumor Necrosis Factor-alpha challenge. The results not only identified stereotypical players in extrinsic apoptotic signaling but two as yet uncharacterized members of the extrinsic apoptotic cascade, Smg7 and Ces2a. We further validated and characterized cell lines containing mutations in these genes against a panel of cell death stimuli and involvement in p53 signaling. In summary, this software enables bench scientists with sensitive data or without access to informatic cores to rapidly interpret results from large scale experiments resulting from pooled CRISPR/Cas9 library screens. The online version of this article (10.1186/s12864-017-4285-2) contains supplementary material, which is available to authorized users.
登录
查看更多内容
ACSL4 通过塑造细胞脂质成分来决定铁死亡敏感性。
影响因子：
14.8
作者：
Doll S;Proneth B;Tyurina YY;Panzilius E;Kobayashi S;Ingold I;Irmler M;Beckers J;Aichler M;Walch A;Prokisch H;Trümbach D;Mao G;Qu F;Bayir H;Füllekrug J;Scheel CH;Wurst W;Schick JA;Kagan VE;Angeli JP;Conrad M
通讯作者：
Conrad M
影响因子：
4.8
作者：
Garneau, D;Revil, T;Chabot, B
通讯作者：
Chabot, B
影响因子：
64.5
作者：
Dixon SJ;Lemberg KM;Lamprecht MR;Skouta R;Zaitsev EM;Gleason CE;Patel DN;Bauer AJ;Cantley AM;Yang WS;Morrison B 3rd;Stockwell BR
通讯作者：
Stockwell BR
影响因子：
64.8
作者：
Konermann S;Brigham MD;Trevino AE;Joung J;Abudayyeh OO;Barcena C;Hsu PD;Habib N;Gootenberg JS;Nishimasu H;Nureki O;Zhang F
通讯作者：
Zhang F
DOI：
10.1038/nrm3454
发表时间：
2012-11
期刊：
Nature reviews. Molecular cell biology
影响因子：
--
作者：
通讯作者：
--