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| Status |
Public on Jan 01, 2020 |
| Title |
CRISPR knockout screening data and RNAsequencing in LINE-1(+) RPE cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
CRISPR knockout screens were performed in RPE cells with or without wildtype p53 function to determine the genetic fitness interactions that occur upon induction of LINE-1 protein expression. We also performed RNAseq analysis in wildtype p53 RPE cells expressing LINE-1 or Luciferase control to determine transcriptomic changes that occur upon LINE-1 expression.
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| Overall design |
Fitness screens are carried out with the Brunello knockout library (76,114 sgRNAs) transduced into RPE cells expressing either LINE-1 vs. eGFP (p53 wildtype cells) or expressing LINE-1 vs. Luciferase (p53 knockdown RPE). The screen in wildtype p53 RPE took place for 19 days, and there are 2 independent biological replicates per expression group. The screen in p53-knockdown RPE took place over 27 days, and there are 6 sequencing timepoints in total with 3 biological replicates per experimental group.
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| Contributor(s) |
Ardeljan D, Steranka JP, Li Z, Taylor MS, Liu C, Payer LM, Sarnecki JS, Wu P, Hruban RH, Boeke JD, Fenyö D, Smogorzewska A, Holland AJ, Burns KH |
| Citation(s) |
32042151 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| F30 CA221175 |
LINE-1 genotoxicity and cytotoxicity and its relevance to cancer |
JOHNS HOPKINS UNIVERSITY |
Daniel Ardeljan |
| P50 GM107632 |
Training Core |
JOHNS HOPKINS UNIVERSITY |
KATHLEEN H BURNS |
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| Submission date |
Sep 14, 2018 |
| Last update date |
Apr 02, 2020 |
| Contact name |
Daniel Ardeljan |
| E-mail(s) |
dardelj1@jhmi.edu
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| Organization name |
Johns Hopkins University School of Medicine
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| Street address |
733 N Broadway, MRB 432
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| City |
Baltimore |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (46)
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| Relations |
| BioProject |
PRJNA491205 |
| SRA |
SRP161806 |
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