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| Status |
Public on Jun 21, 2018 |
| Title |
miRNA expression profiles of HeLa-Cas9 and NCI-N87 cells |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
MicroRNAs (miRNAs) play an important role in the regulation of gene expression and are often dysregulated in disease. The recent development of the CRISPR-Cas9 gene-editing system, composed of the Cas9 nuclease in complex with a single guide RNA (sgRNA), allows researchers to direct DNA cleavage at a predetermined site and to conduct genome-scale knockout screens. To determine the functional role of miRNAs in cancer, we designed and constructed a library of 7,382 sgRNAs to target 85% of the 1,881 annotated human miRNA stem-loops. We then examined the role of miRNAs in HeLa cell fitness by monitoring the change in frequency of each sgRNA over time. We identified 44 pro-proliferative miRNAs from two replicate experiments, including miR-31, a known cervical cancer overexpressing miRNA that enhances HeLa cell proliferation. We also examined the role of miRNAs in NCI-N87 gastric cancer cells and identified 10 pro-fitness and 10 anti-fitness miRNAs. In both screens, many of the pro-fitness miRNAs identified are overexpressed in tumors cervical tumors for HeLa or gastric tumors for NCI-N87. In summary, we present a CRISPR miRNA-targeted screen which was able to identify both known and novel fitness-associated miRNAs in the HeLa and NCI-N87 cell lines.
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| Overall design |
The miRNA expression profile of NCI-N87 gastric cancer cells was determined by high throughput miRNA sequencing (NCI-N87_miR-seq). To determine the miRNA expression profile of the clonal HeLa-Cas9 cell line, we determined the miRNA expression in HeLa-Cas9 cells 9 days after transduction with the LX-miR library for two biological replicates (HeLa_1D7_miR-seq and HeLa_2D7_miR-seq). To examine the impact of doxycycline treatment on miRNA expression, we also profiled the miRNA expression in HeLa-Cas9 cells with (HeLa_1D22G1_miR-seq) and without (HeLa_1D22md_miR-seq) doxycycline treatment.
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| Contributor(s) |
Kurata JS, Lin R |
| Citation(s) |
29720387 |
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| Submission date |
Feb 19, 2018 |
| Last update date |
Mar 27, 2019 |
| Contact name |
Ren-Jang Lin |
| E-mail(s) |
[email protected]
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| Organization name |
City of Hope
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| Department |
Molecular and Cellular Biology
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| Street address |
1500 E Duarte Rd
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| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (5)
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| Relations |
| BioProject |
PRJNA434552 |
| SRA |
SRP133052 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE110784_HeLa_and_NCI-N87_Read_Counts.csv.gz |
17.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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