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| Status |
Public on Aug 14, 2021 |
| Title |
STAMPScreen: An Integrated Pipeline for Mammalian Genetic Screening |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
With the recent advancements in genome editing, next generation sequencing (NGS), and scalable cloning techniques, scientists can now conduct genetic screens at unprecedented levels of scale and precision. With such a multitude of technologies, there is a need for a simple yet comprehensive pipeline to enable systematic mammalian genetic screening. In this study, we develop novel algorithms for target identi fication and a toxin-less Gateway cloning tool, termed MegaGate, for library cloning which, when combined with existing genetic perturbation methods and NGS-coupled readouts, enable versatile engineering of relevant mammalian cell lines. Our integrated pipeline for Sequencing-based Target Ascertainment and Modular Perturbation Screening (STAMPScreen) can thus be utilized for a host of cell state engineering applications.
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| Overall design |
4 independent biological samples are analyzed. GFP or ZGLP1 was induced via docycyline in female hiPSCs in biological duplicates. GFP is used as a control for ZGLP1 induction.
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| Contributor(s) |
Kramme C, Plesa AM, Wang HH, Wolf B, Smela MP, Guo X, Kohman RE, Chatterjee P, Church GM |
| Citation(s) |
35474898 |
| Submission date |
Aug 13, 2021 |
| Last update date |
May 05, 2022 |
| Contact name |
George Church |
| Organization name |
Harvard Medical School
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| Department |
Genetics
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| Lab |
George Church
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| Street address |
CLS, 528/7A, 3 Blackfan Cir.
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| City |
BOSTON |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA754432 |
| SRA |
SRP332485 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE182088_DESeq2_ZGLP1_GFP.csv.gz |
732.6 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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