Embyronic Stem Cell Data

Kevin Wang

12 Apr 2024

Source: vignettes/case_study/ESC_Data.Rmd

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

Monocle2 cell trajectory plot

Integrated scMerge data