Neuronal Single Cell Data

Kevin Wang

12 Apr 2024

Introduction

This is a mouse neuronal single-cell data comprising of 2 different experiments.

Integration challenge

• Prior to integration, there is a strong separation effect by experiments and batches.

Data description

• Data source:

Type of merge		Name		ID	Author	DOI or URL	Protocol	Organism	Tissue	# of cell types	# of cells	# of batches
Across different experiments		Neuronal		SRP065920	Tan	10.15252/msb.20156639	Smart‐Seq2	Mouse	Neuronal	2	145	NA
				GSE75413	Hanchate	10.1126/science.aad2456	STRT-seq

• Relation to the scMerge article: Supplementary Figure 10.

Data visualisation

tSNE plots by cell types and batch

Integrated scMerge data

• Data availability: Mouse Neuronal Data (in RData format)

• scMerge parameters for integration:

  • Unsupervised scMerge
  • kmeans K = (2,2)
  • Negative controls are mouse scSEG