Welcome to the CESCG Stem Cell Hub!

Welcome to the Stem Cell Hub web site. This contains high quality genomics data from a wide range of stem cell projects. It was built with funding from the California Institute of Regenerative Medicine (CIRM), and includes all the data from two dozen labs participating in CIRM's Center of Excellence for Stem Cell Genomics as well as selected data from other relevant stem cell projects. It includes single cell RNA-seq data on naturally developing human tissues as well as cells engineered from healthy skin and blood cells to become replacements for diseased cells and tissues, including data from ethically and scientifically careful human clinical trials.

The Stem Cell Hub combines state of the art software with careful human curation. The software runs quality checks that ensure the data is in the proper format, contains no contamination, that the DNA aligns in expected places, that the level of mitochondrial and ribosomal data are within expected range, and gathers statistics on how well replicates agree using a number of statistical measures. The system supports tagging

the data using a flexible metadata system that allows experiments to be described in a concise but rich manner that reflects any natural hierarchies or control/experiment groups that are part of the experimental design. The human curators work with the contributing labs and the system to make sure that experiments are described consistently across labs and that metadata tags exist to describe even new, leading edge assays. The Stem Cell Hub can be searched using either a faceted search or SQL like queries on the metadata. The Hub can restrict access to certain data to specific users to meet privacy requirements.

We hope that the Stem Cell Hub will be useful to a wide range of scientists from clinicians to cell biologists to bioinformaticians doing custom analysis and combining data from multiple projects. Please see the help link for additional information on how to use the site.