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Single-cell transcriptomes of fluorescent, ubiquitination-based cell cycle indicator cells

By Michael Böttcher, Tsukasa Kouno, Elo Madissoon, Efthymios Motakis, Imad Abugessaisa, Sachi Kato, Harukazu Suzuki, Yoshihide Hayashizaki, Takeya Kasukawa, P. Carninci, Timo Lassmann, Jay W Shin, Charles Plessy

Posted 15 Dec 2016
bioRxiv DOI: 10.1101/088500

We used a transgenic HeLa cell line that reports cell cycle phases through fluorescent, ubiquitination-based cell cycle indicators (Fucci), to produce a reference dataset of more than 270 curated single cells. Microscopic images were taken from each cell followed by RNA-sequencing, so that single-cell expression data is associated to the fluorescence intensity of the Fucci probes in the same cell. We developed an open data management and quality control workflow that enables users to replicate the processing of the sequence and microscopic image data that we deposited in public repositories. The workflow outputs a table with metadata, that is the starting point for further studies on these data. Beyond its use for cell cycle studies, We also expect that our workflow can be adapted to other single-cell projects using a similar combination of sequencing data and fluorescence measurements.

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