Oocytes, a single cell and a tissue

Development of single cell sequencing allows detailing the transcriptome of individual oocytes. Here, we compare different RNA-seq datasets from single and pooled mouse oocytes and show higher reproducibility using single oocyte RNA-seq. We further demonstrate that UMI (unique molecular identifiers) based and other deduplication methods are limited in their ability to improve the precision of these datasets. Finally, for normalization of sample differences in cross-stage comparisons, we propose that external spike-in molecules are comparable to using the endogenous genes stably expressed during oocyte maturation. The ability to normalize data among single cells provides insight into the heterogeneity of mouse oocytes. To confirm the ERCC normalization, we performed mouse single oocyte RNA-seq with different amplification cycles during library preparation and also different fractions of GV oocytes (1/2, 1/4, 1/8).