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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 31, 2023 |
| Title |
CRISPR/Cas9 genome-wide screen and transcriptome profiling in a MYC-conditional HCC model [EC4 RNA-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The MYC oncogene is often dysregulated in human cancer, including hepatocellular carcinoma (HCC). However, MYC is considered undruggable to date. Here, we comprehensively identify genes essential for the survival of MYC-high but not MYC-low cells by performing a CRISPR/Cas9 genome-wide screen in a MYC-conditional HCC model. Our screen identifies novel MYC-synthetic lethal interactions, as well as most previously identified MYC-synthetic lethal genes. In particular, we found genes involved in nuclear to cytoplasmic transport to be MYC-synthetic lethal in HCC, and we show that many of these genes are transcriptionally upregulated in MYC-high murine HCC.
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| Overall design |
RNA sequencing was performed on conditional MYC-HCC-derived mouse cells (EC4 cells) with MYC expression conditionally controlled by doxycycline.
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| Contributor(s) |
Deutzmann A, Li Y, Dhanasekaran R, Sullivan DK |
| Citation(s) |
38302473 |
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| Submission date |
Jul 26, 2022 |
| Last update date |
Feb 04, 2024 |
| Contact name |
Dean Felsher |
| E-mail(s) |
dfelsher@stanford.edu
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| Organization name |
Stanford University
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| Department |
Medicine
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| Lab |
Felsher Lab
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| Street address |
269 Campus Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (9)
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| GSM6398474 |
HCC cells, day 1 (+dox), rep 1 |
| GSM6398475 |
HCC cells, day 1 (+dox), rep 2 |
| GSM6398476 |
HCC cells, day 1 (+dox), rep 3 |
| GSM6398477 |
HCC cells, day 7 (+dox), rep 1 |
| GSM6398478 |
HCC cells, day 7 (+dox), rep 2 |
| GSM6398479 |
HCC cells, day 7 (+dox), rep 3 |
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| This SubSeries is part of SuperSeries: |
| GSE205132 |
CRISPR/Cas9 genome-wide screen and transcriptome profiling in a MYC-conditional HCC model |
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| Relations |
| BioProject |
PRJNA862493 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE209798_rnaseq.count.txt.gz |
736.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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