Bioinformatics portal

HEAT MAPOur laboratory performs global transcriptomic profiling to understand the genetic programs of our cells. While all our published datasets are available for free download from the gene expression omnibus (GEO), we also provide interactive websites and processed biostatistical analyses for free use through this web portal. Please enjoy and feel free to share the microarray, population-based RNA-Seq, and single cell RNA-Seq profiles below. If you find something interesting, let us know!

Click here to access all our raw datasets through GEO

To interact with our latest microarray and single cell RNA-Seq data, click on an entry below:

1. Access our RNA-Seq data from our time series including iAEC2s, published by Jacob et al in Cell Stem Cell 2017

2. Download an excel file (42MB) with human iPSC time-series biostatistics from our Microarray profiling of major stages of the lung directed differentiation protocol (published in Hawkins et al. JCI 2017.)

3. Interact with our human iPSC-derived lung single cell RNA-Seq analyses through either:

A: The Cincinnati LGEA (Lung Gene Expression Analysis) web portal or…

B: Ian Driver’s interactive Monocle tool to look up your favorite gene in our published Monocle analysis of iPSC-derived NKX2-1+ lung progenitors (Hawkins JCI 2017; BE SURE TO TYPE YOUR GENE NAME IN CAPS ONLY).

Other analyses from our published papers:

  1. Mouse ESC-derived Nkx2-1+ sorted lung vs thyroid progenitors (Serra/Kotton. Development 2017)
  2. hiPSC/ESC hepatic directed differentiation time series analyses (Affy arrays): as published in Wilson/Kotton Stem Cell Reports 2015. Download an an excel file of the time series computational analysis (33MB). Or access the GEO raw data.
  3. Mouse ESC/iPSC definitive endoderm directed differentiation (Christodoulou, JCI 2011)
  4. Mouse in vivo fetal developing definitive endoderm
  5. Human clone to clone hiPSC variability: impact on blood differentiation efficiency
  6. Mouse ESC derived Nkx2-1GFP mixed lung/thyroid cells (Longmire/Kotton Cell Stem Cell 2012).