In SydneyBioX/scMerge: scMerge: Merging multiple batches of scRNA-seq data

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

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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