Transcriptional signatures in iPSC-derived neurons are reproducible across labs when differentiation protocols are closely matched

Reproducibility of expression patterns in iPSC-derived cells from different labs is an important first step in ensuring replication of biochemical or functional assays that are performed in different labs. Here we show that reproducible gene expression patterns from iPSCs and iPSC-derived neurons matured and collected at two separate laboratory locations can be achieved by closely matching protocols and reagents. While there are significant differences in gene expression between iPSCs and differentiated neurons, as well as between different donor lines of the same cell type, transcriptional changes that vary with laboratory sites are relatively small. These results suggest that making great efforts to match protocols, reagents and technical methods between labs may improve the reproducibility of iPSC-derived cell models. We used two different iPSC donor lines at two laboratory sites. 33i N=3, CS25i N=2. Cells were partially differentiated in forebrain neurons at one site then half were shipped to the second lab. Partially differentiated cells were thawed and matured in both labs starting on the same day. We collected RNA from iPSC and iPSC derived neurons from each line at each site. Differential expression analysis was done to identify sources of variance.