Scientists at the University of Wisconsin-Madison have launched an open-access database for collecting and analyzing quantitative information about pluripotent stem cells, including data on mRNA, protein, and post-translational modifications.
Named the Stem Cell -Omics Repository, the resource was launched this week to coincide with a study published in Nature Methods comparing the proteomes and phosphoproteomes of human embryonic and induced pluripotent stem cells.
In addition to providing this protein-level comparison, the paper lays out a proteomic workflow using a relatively large number of samples and biological replicates to draw out subtle but potentially important differences between similar cell types, said study leader Joshua Coon, UW-Madison assistant professor
For the stem-cell work the researchers “combined high accuracy mass spectrometry and isobaric tagging on a large scale” in a way that let them compare proteins and phosphorylation sites across four ESC lines and four iPSC lines in biological triplicate. This enabled them to identify differences between the lines that would otherwise have gone undetected.