Details

Autor(en) / Beteiligte

• Choi, Jarny
• Butcher, Suzanne K.
• Angel, Paul W.
• Bransfield, Jack
• Barry, Jake
• Faux, Noel
• Shaban, Bobbie
• Pillai, Priyanka
• Michalewicz, Aleks
• Wells, Christine A.

Titel

Stemformatics data portal enables transcriptional benchmarking of lab-derived myeloid cells

Ist Teil von

• Stem cell reports, 2024-06, Vol.19 (6), p.922-932

Ort / Verlag

United States: Elsevier Inc

Erscheinungsjahr

2024

Quelle

MEDLINE

Beschreibungen/Notizen

• Stemformatics.org has been serving the stem cell research community for over a decade, by making it easy for users to find and view transcriptional profiles of pluripotent and adult stem cells and their progeny, comparing data derived from multiple tissues and derivation methods. In recent years, Stemformatics has shifted its focus from curation to collation and integration of public data with shared phenotypes. It now hosts several integrated expression atlases based on human myeloid cells, which allow for easy cross-dataset comparisons and discovery of emerging cell subsets and activation properties. The atlases are designed for external users to benchmark their own data against a common reference. Here, we use case studies to illustrate how to find and explore previously published datasets of relevance and how in-vitro-derived cells can be transcriptionally matched to cells in the integrated atlas to highlight phenotypes of interest. [Display omitted] •Stemformatics.org hosts over 430 high-quality expression datasets•Integrated atlases show the comparison between in-vitro- and in-vivo-derived blood cells•Helps users compare data generated across laboratories, methods, or cell sources In this article, Wells and colleagues describe the Stemformatics reference atlases, which provide fast and intuitive comparisons of a user’s own stem cell data against primary human myeloid cells. The toolkit supports comparison to tissue-resident or disease-associated myeloid cells, including heatmaps of major cellular pathways.