Assessment of stem cell differentiation based on genome-wide expression profiles.

In recent years, protocols have been established to differentiate stem and precursor cells into more mature cell types. However, progress in this field has been hampered by difficulties to assess the differentiation status of stem cell-derived cells in an unbiased manner. Here, we present an analysis pipeline based on published data and methods to quantify the degree of differentiation and to identify transcriptional control factors explaining differences from the intended target cells or tissues. The pipeline requires RNA-Seq or gene array data of the stem cell starting population, derived 'mature' cells and primary target cells or tissue. It consists of a principal component analysis to represent global expression changes and to identify possible problems of the dataset that require special attention, such as: batch effects; clustering techniques to identify gene groups with similar features; over-representation analysis to characterize biological motifs and transcriptional control factors of the identified gene clusters; and metagenes as well as gene regulatory networks for quantitative cell-type assessment and identification of influential transcription factors. Possibilities and limitations of the analysis pipeline are illustrated using the example of human embryonic stem cell and human induced pluripotent cells to generate 'hepatocyte-like cells'. The pipeline quantifies the degree of incomplete differentiation as well as remaining stemness and identifies unwanted features, such as colon- and fibroblast-associated gene clusters that are absent in real hepatocytes but typically induced by currently available differentiation protocols. Finally, transcription factors responsible for incomplete and unwanted differentiation are identified. The proposed method is widely applicable and allows an unbiased and quantitative assessment of stem cell-derived cells.This article is part of the theme issue 'Designer human tissue: coming to a lab near you'.

The chilean network of microbial culture collections: establishment and operation / Red chilena de colecciones de cultivos microbianos: establecimiento y operación

According to the data available at the World Data Center for Microorganism-WDCM from the World Federation for Culture Collection-WFCC, Chile has four registered culture collections that preserve 2777 microbial strains. At the global point of view, the culture collections in Chile are in different level of operation regarding its own infrastructure and compliancy with quality standards for preservation of strains and for services provide. The absence of funding to support the preservation of the Chilean microbial assets is a key issue for the development of the Chilean bioeconomy. Considering this, the Chilean culture collections started working together to establish the Chilean Network of Microbial Culture Collections (RCCCM, acronym in Spanish). In this note, the establishment and operation of the RCCCM is presented and discussed.

De acuerdo con los datos disponibles en el World Data Center for Microorganism-WDCM de la Federación Mundial para la Colección de Cultivos - WFCC, Chile tiene cuatro colecciones de cultivos registradas que preservan 2777 cepas microbianas. Desde el punto de vista global, las colecciones de cultivos en Chile se encuentran en diferentes niveles de operación con respecto a su propia infraestructura y cumplimiento con estándares de calidad para la preservación de las cepas y para los servicios que proporcionan. La ausencia de financiamiento para apoyar la preservación de los activos microbianos chilenos es un tema clave para el desarrollo de la bioeconomía chilena. Considerando esto, las colecciones chilenas de cultivos comenzaron a trabajar conjuntamente para establecer la Red Chilena de Colecciones de Cultivos Microbianos (RCCCM). En esta nota se presenta y discute el establecimiento y funcionamiento de la RCCCM.