@article {Dueck045450, author = {Hannah R. Dueck and Rizi Ai and Adrian Camarena and Bo Ding and Reymundo Dominguez and Oleg V. Evgrafov and Jian-Bing Fan and Stephen A. Fisher and Jennifer S. Hernstein and Tae Kyung Kim and Jae Mun (Hugo) Kim and Ming-Yi Lin and Rui Liu and William J. Mack and Sean McGroty and Joseph Nguyen and Neeraj Salathia and Jamie Shallcross and Tade Souaiaia and Jennifer Spaethling and Chris P. Walker and Jinhui Wang and Kai Wang and Wei Wang and Andre Wilberg and Lina Zheng and Robert H. Chow and James Eberwine and James A. Knowles and Kun Zhang and Junhyoung Kim}, title = {Assessing the measurement transfer function of single-cell RNA sequencing}, elocation-id = {045450}, year = {2016}, doi = {10.1101/045450}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Recently, measurement of RNA at single cell resolution has yielded surprising insights. Methods for single-cell RNA sequencing (scRNA-seq) have received considerable attention, but the broad reliability of single cell methods and the factors governing their performance are still poorly known. Here, we conducted a large-scale control experiment to assess the transfer function of three scRNA-seq methods and factors modulating the function. All three methods detected greater than 70\% of the expected number of genes and had a 50\% probability of detecting genes with abundance greater than 2 to 4 molecules. Despite the small number of molecules, sequencing depth significantly affected gene detection. While biases in detection and quantification were qualitatively similar across methods, the degree of bias differed, consistent with differences in molecular protocol. Measurement reliability increased with expression level for all methods and we conservatively estimate the measurement transfer functions to be linear above ~5-10 molecules. Based on these extensive control studies, we propose that RNA-seq of single cells has come of age, yielding quantitative biological information.}, URL = {https://www.biorxiv.org/content/early/2016/03/24/045450}, eprint = {https://www.biorxiv.org/content/early/2016/03/24/045450.full.pdf}, journal = {bioRxiv} }