This is a mouse embryonic stem cell (mESC) single-cell data comprising of 3 different batches from a single experiment.

Integration challenge

  • Prior to integration, there is a strong separation effect by batches.
  • This data is relatively simple with only the usual batch effects within an experiment. Hence, in the scMerge article it was used as an illustrative example for various aspects of the methodology and also included as an example dataset in our package.

Data description

  • Data source:
Type of merge Name ID Author DOI or URL Protocol Organism Tissue # of cell types # of cells # of batches
Within experiment mESC E-MTAB-2600 Kolodziejczyk 10.1016/j.stem.2015.09.011 SMARTer/C1 Mouse Mouse ESC 3 704 5
  • Relation to the scMerge article: Main Figure 1, Supplementary Figure 6 and 17.

Data visualisation

tSNE plots by cell types and batch

Illustrating the robustness of the parameters \(k_{RUVIII}\) and \(k_{Cluster}\)

Integrated scMerge data