PT  - JOURNAL ARTICLE
AU  - Morten Seirup
AU  - Li-Fang Chu
AU  - Srikumar Sengupta
AU  - Ning Leng
AU  - Christina M. Shafer
AU  - Bret Duffin
AU  - Angela L. Elwell
AU  - Jennifer M. Bolin
AU  - Scott Swanson
AU  - Ron Stewart
AU  - Christina Kendziorski
AU  - James A. Thomson
AU  - Rhonda Bacher
TI  - Tradeoff between more cells and higher read depth for single-cell RNA-seq spatial ordering analysis of the liver lobule
AID  - 10.1101/764191
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 764191
4099  - http://biorxiv.org/content/early/2019/09/11/764191.short
4100  - http://biorxiv.org/content/early/2019/09/11/764191.full
AB  - As single-cell experiments generate increasingly more cells at reduced sequencing depths, the value of a higher read depth may be overlooked. Using data from two contrasting single-cell RNA-seq protocols that lend themselves to having either higher read depth (Smart-seq) or many cells (MARS-seq) we evaluate the trade-offs in the context of pseudo-spatial reconstruction of the liver lobule. Overall, we find gene expression profiles after spatial-reconstruction analysis are highly reproducible between datasets. Smart-seq’s higher sensitivity and read-depth allows analysis of lower expressed genes and isoforms. Our analysis emphasizes the importance of selecting a protocol based on the biological questions and features of interest. Additionally, by performing subsampling analyses we evaluate trade-offs for each protocol and illustrate that optimizing the balance between sequencing depth and number of cells within a protocol is important for efficient use of resources.