MiRNA expression profiles of HeLa-Cas9 and NCI-N87 cells
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ABSTRACT:
PROVIDER: PRJNA434552 | ENA |
REPOSITORIES: ENA
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Project description: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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The current database comprises a very high proteome coverage (more than half of human genome) and serves as a reference expression profiles of NCI-60 cell line panel. As such it contains details about protein and peptide identifications together with the corresponding fragment spectra and quantitative information. It also contains chromosome-centric view to identify the abundance and distribution of proteins whose genes are co-located on the same chromosome. In addition, a simple interface allows to query for differential protein expression either by protein names or attributes such as ontology terms. The protein queries return the cell lines where protein expression has been reported.
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