iCSDB: An integrated database of CRISPR screens

Ahyoung Choi, Insu Jang, Heewon Han, Min Seo Kim, Jinhyuk Choi, Jieun Lee, Sung Yup Cho, Yukyung Jun, Charles Lee, Jaesang Kim, Byungwook Lee, Sanghyuk Lee

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

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/.

Original languageEnglish
Pages (from-to)D956-D961
JournalNucleic Acids Research
Volume49
Issue numberD1
DOIs
StatePublished - 8 Jan 2021

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