Mouse Embryonic Stem Cell Data

Kevin Wang

12 Apr 2024

Introduction

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

• Data availability: Unmerged data (in RData format) and mouse ESC Data (in RData format)

• scMerge parameters for integration:

  • Unsupervised scMerge
  • kmeans K = (1,3,3,1,1)
  • Negative controls are mouse scSEG