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

Introduction

This is an inter-organism single-cell embryonic stem cell (ESC) data comprising of 8 different experiements across 2 (human + mouse) organisms.

Integration challenge

• The data is comprising of both human and mouse ESC data, this inter-organism integration is challenging from both a technical and biological perspective.
• Prior to integration, there is a strong separation effect by different experiments.
• Another batch effect is the different protocols with significant depth differences.

Data description

• Data source:

| Type of merge | Name | ID | Author | DOI or URL | Protocol | Organism | Tissue | # of cell types | # of cells | # of batches | |------------------|------|-------------|-------------|----------------------------|--------------------|---------------|-----------------|-----------------|------------|-------------------| | Across Organisms | ESC | GSE84133 | Baron | 10.1016/j.cels.2016.08.011 | inDrop | Human+ mouse | Pancreas Islets | 13 | 8569 | 2 (human & mouse) | | | | GSE45719 | Deng | 10.1126/science.1245316 | Smart-Seq | Mouse | ESC | 10+ | 2144 | NA | | | | GSE57249 | Biase | 10.1101/gr.177725.114 | SMARTer | | | | | | | | | E-MTAB-3321 | Goolam | 10.1016/j.cell.2016.01.047 | Smart-Seq2 | | | | | | | | | GSE44183 | Xue | 10.1038/nature12364 | Tang et al., 2010 | Human + mouse | | | | | | | | E-MTAB-3929 | Petropoulos | 10.1016/j.cell.2016.03.023 | Smart-Seq2 | human | | | | | | | | GEO66507 | Blakeley | 10.1242/dev.123547 | SMARTer | | | | | | | | | GSE36552 | Yan | 10.1038/nsmb.2660 | Than et al., 2010 | | | | | |

• Relation to the scMerge article: Main Figure 3d.

Data visualisation

PCA plots by cell types and batch

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Monocle2 cell trajectory plot

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Integrated scMerge data

• Data availability: ESC Data (in RData format)

• scMerge parameters for integration:

SydneyBioX/scMerge documentation built on April 14, 2024, 3:22 a.m.