Pancreas 4 Data

Kevin Wang

12 Apr 2024

Source: vignettes/case_study/Pancreas4_Data.Rmd

Introduction

This is a human pancreas single-cell data comprising of 4 experiments.

Integration challenge

  • Prior to integration, there is a strong separation effect by experiments.
  • In addition, there are 3 different protocols, the sequencing depths poses an extra challenge.
  • With 4,566 cells, this data poses a moderate dimensionality challenge to data integration.

Data description

  • Data source:
Type of merge Name ID Author DOI or URL Protocol Organism Tissue # of cell types # of cells # of batches
Across platforms with significant depth difference Pancreas4 GSE81608 Xin 10.1016/j.cmet.2016.08.018 SMARTer/C1 Human Pancreas 6 4566 NA
GSE83139 Wang 10.2337/db16-0405 Smart-Seq
GSE86469 Lawlor 10.1101/gr.212720.116 SMARTer/C1
E-MTAB-5061 Segerstolpe 10.1016/j.cmet.2016.08.020 Smart-Seq2
  • Relation to the scMerge article: Supplementary Figure 4 and 5.

Data visualisation

PCA plots by cell types and batch

RLE plots and percentage of explained variance plots

Integrated scMerge data

  • Data availability: Pancreas4 (in RData format)

  • scMerge parameters for integration:

    • Unsupervised scMerge
    • kmeans K = (4,6,6,6)
    • Negative controls are human scSEG