Stemformatics: helping researchers tackle big research questions

Stemformatics, an online gene expression data portal, was established in 2011 by Professor Christine Wells and her team as part of Stem Cells Australia, to assist biologists visually explore data, identify cell-type restricted genes and compare gene expression in multiple cells and tissues.

As new technologies arise, stem cells are being characterized at a far more detailed scale than ever. This data creates challenges for the stem cell research community, including finding and navigating data that is both reliable and relevant to the biological question at hand.

Stemformatics, an online gene expression data portal, was established in 2011 by Professor Christine Wells and her team as part of Stem Cells Australia, to assist biologists visually explore data, identify cell-type restricted genes and compare gene expression in multiple cells and tissues.

Stemformatics contains over 420 public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Developed for the stem cell community, it has a major focus on pluripotency, tissue stem cells, and staged differentiation.

Stemformatics also supports cross-laboratory collaborative activities and many research projects have come together using Stemformatics as the main research platform. One such project is Leukomics, a virtual platform that could help researchers find a cure for multiple types of leukemia, through easy access to data from relevant samples generated by laboratories around the world.

To ensure that Stemformatics data is of high quality and has been processed in a consistent manner, Stemformatics uses a stringent set of quality control metrics. This means that about 30% of datasets processed by Stemformatics fail the quality control metrics and never make it to the portal.

Stemformatics also hosts a wide range of data visualisation tools, which enable researchers to explore the data and come up with hypotheses.

Every year over 4000 researchers from 6 continents use Stemformatics. This unique and powerful resource for the stem cell research community is freely available at www.stemformatics.org, and is at the forefront of research, tackling big research questions.

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Jarny Choi

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