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iCSDB: An integrated database of CRISPR screens

Title
iCSDB: An integrated database of CRISPR screens
Authors
Choi A.Jang I.Han H.Kim M.-S.Choi J.Lee J.Cho S.-Y.Jun Y.Lee C.Kim J.Lee B.Lee S.
Ewha Authors
이상혁김재상Charles Lee
SCOPUS Author ID
이상혁scopus; 김재상scopus; Charles Leescopus
Issue Date
2021
Journal Title
Nucleic Acids Research
ISSN
0305-1048JCR Link
Citation
Nucleic Acids Research vol. 49, no. D1, pp. D956 - D961
Publisher
Oxford University Press
Indexed
SCIE; SCOPUS WOS scopus
Document Type
Article
Abstract
High-throughput screening based on CRISPR-Cas9 libraries has become an attractive and powerful technique to identify target genes for functional studies. However, accessibility of public data is limited due to the lack of user-friendly utilities and up-to-date resources covering experiments from third parties. Here, we describe iCSDB, an integrated database of CRISPR screening experiments using human cell lines. We compiled two major sources of CRISPR-Cas9 screening: the DepMap portal and BioGRID ORCS. DepMap portal itself is an integrated database that includes three large-scale projects of CRISPR screening. We additionally aggregated CRISPR screens from BioGRID ORCS that is a collection of screening results from PubMed articles. Currently, iCSDB contains 1375 genome-wide screens across 976 human cell lines, covering 28 tissues and 70 cancer types. Importantly, the batch effects from different CRISPR libraries were removed and the screening scores were converted into a single metric to estimate the knockout efficiency. Clinical and molecular information were also integrated to help users to select cell lines of interest readily. Furthermore, we have implemented various interactive tools and viewers to facilitate users to choose, examine and compare the screen results both at the gene and guide RNA levels. iCSDB is available at https://www.kobic.re.kr/icsdb/. © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
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DOI
10.1093/nar/gkaa989
Appears in Collections:
자연과학대학 > 생명과학전공 > Journal papers
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