Fig. 1.

Subcellular fractionation of secretory pathway organelles was carried out from hESCs and MEFs. Distribution of proteins annotated to the secretory pathway organelles (endoplasmic reticulum, GO:0005783, endoplasmic reticulum-Golgi intermediate compartment, GO:0005793; ER to Golgi transport vesicle, GO:0030134; Golgi apparatus, GO:0005794; secretory granule, GO:0030141; transport vesicle, GO:0030133; and ribosome, GO:0005840) are shown for (A) H1 hESCs, (B) H9 hESCs, and (C) MEFs. GO enrichment analysis for identified proteins was carried out using DAVID, and statistically significant enrichment for secretory pathway organelles was obtained for (D) H1 hESCs, (E) H9 hESCs, and (F) MEFs. G, fractional abundance of various organelles in the whole cell lysate and subcellular fractions putatively enriched in secretory pathway organelles, obtained from H9 hESCs. “Secretory cargo” denotes proteins that are annotated as secreted in the Uniprot database. “Extracellular” refers to proteins annotated as extracellular (GO:0031012, GO:0005576, GO:0044421, GO:0005615, and GO:0005578). Secretory pathway organelles and mitochondria are considered a part of the cytoplasm, and many plasma membrane and nuclear proteins are also annotated as cytoplasmic. Therefore, proteins that were already accounted for in these organelles were not included in the category “remaining cytoplasm.”