title: Analysis of image-based phenotypic parameters for high throughput gene perturbation assays.
abstract: Although image-based phenotypic assays are considered a powerful tool for siRNA library screening, the reproducibility and biological implications of various image-based assays are not well-characterized in a systematic manner. Here, we compared the resolution of high throughput assays of image-based cell count and typical cell viability measures for cancer samples. It was found that the optimal plating density of cells was important to obtain maximal resolution in both types of assays. In general, cell counting provided better resolution than the cell viability measure in diverse batches of siRNAs. In addition to cell count, diverse image-based measures were simultaneously collected from a single screening and showed good reproducibility in repetitions. They were classified into a few functional categories according to biological process, based on the differential patterns of hit (i.e., siRNAs) prioritization from the same screening data. The presented systematic analyses of image-based parameters provide new insight to a multitude of applications and better biological interpretation of high content cell-based assays.
authors.affiliation: Center for Advanced Bioinformatics & Systems Medicine, Sookmyung Women's University, Seoul 140-742, Republic of Korea. Electronic address: mee0908@hanmail.net.
authors.forename: Mee
authors.initials: M
authors.lastname: Song
authors.affiliation: Center for Advanced Bioinformatics & Systems Medicine, Sookmyung Women's University, Seoul 140-742, Republic of Korea. Electronic address: eajeong@sookmyung.ac.kr.
authors.forename: Euna
authors.initials: E
authors.lastname: Jeong
authors.affiliation: Discovery Biology Group, Institute Pasteur Korea, Seongnam-si, Gyeonggi-do 463-400, Republic of Korea. Electronic address: taekyu82@naver.com.
authors.forename: Tae-Kyu
authors.initials: TK
authors.lastname: Lee
authors.affiliation: Imaging Processing Platform, Institute Pasteur Korea, Seongnam-si, Gyeonggi-do 463-400, Republic of Korea. Electronic address: yury.tsoy@ip-korea.org.
authors.forename: Yury
authors.initials: Y
authors.lastname: Tsoy
authors.affiliation: Discovery Biology Group, Institute Pasteur Korea, Seongnam-si, Gyeonggi-do 463-400, Republic of Korea. Electronic address: yjkwonipk@gmail.com.
authors.forename: Yong-Jun
authors.initials: YJ
authors.lastname: Kwon
authors.affiliation: Center for Advanced Bioinformatics & Systems Medicine, Sookmyung Women's University, Seoul 140-742, Republic of Korea; Department of Biological Sciences, Sookmyung Women's University, Seoul 140-742, Republic of Korea. Electronic address: yoonsj@sookmyung.ac.kr.
authors.forename: Sukjoon
authors.initials: S
authors.lastname: Yoon
mesh_terms: D002452:Cell Count; D045744:Cell Line, Tumor; D002470:Cell Survival; D057166:High-Throughput Screening Assays; D006801:Humans; D007091:Image Processing, Computer-Assisted; D010641:Phenotype; D034741:RNA, Small Interfering / Q000235:genetics
chemical_list: D034741:RNA, Small Interfering
keywords: Gene perturbation; Image-based assay; Phenotypic parameter; siRNA screening