Last updated: 2020-10-19

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Knit directory: Embryoid_Body_Pilot_Workflowr/analysis/

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Welcome! This is a research website detailing analyses analyses performed on scRNA-seq data from human embryoid bodies, aggregates of spontaneously differentiating cells generated from induced pluripotent stem cells.

The overarching goals of this work are to:

  1. characterize tthe diversity of cell types resulting from this particular differentiation protocol
  2. Understand the contribution of biological and technical variation present in all levels of this this type of data i)What is the relative contribution of individual and replicate to variation in cell composition?
  1. What is the relative contribution of individual and replicate to variation in gene expression?
  2. What is the relative contribution of individual and replicate to variation in gene expression dynamics across distinct developmental trajectories?
  1. Evaluate the future prospects of this model system (EBs + single cell) for identification of dynamic QTLs

Study Design:

Embryoid bodies were formed from 3 human iPSCs lines in 3 replicates. Three weeks after formation, EBs were dissociated and scRNA-seq data was collected using the 10x platform. After quality control and filtering, this dataset consists of 42,488 cells.

Preprocessing, QC, and filtering

  • to be added soon!

Run EmptyDrops, Add Metadata to Seurat object from each 10x lane

  • to be added soon!

Differential Expression with limma (Pseudobulk)

Seurat subclustering

  • To be added soon!

Cell type identification using scHCL

Topic Modelling with FastTopics

  • to be added soon!

Variance Partition (to determine the relative contribution of Cluster, Batch, and Individual to variation in gene expression)

Trajectory Inference with Scanpy/PAGA

  • to be added soon!

Identification/Exploration of Dynamic Gene Module with Split-GPM

  • Link to Josh Popp's github to be added soon