slowkow / fibrotime

:tangerine: View the gene expression response to TNF and IL-17A with vanilla Javascript and HTML.

fibrotime

Explore the gene expression response to tumor necrosis factor (TNF) and interleukin 17 (IL-17A). Our data includes experiments with time series, dose response, and gene silencing.

🚀 Explore the data

https://immunogenomics.io/fibrotime

🎓 Read the paper

CUX1 and IκBζ mediate the synergistic inflammatory response to TNF and IL-17A in stromal fibroblasts

Kamil Slowikowski, Hung N. Nguyen, Erika H. Noss, Daimon P. Simmons, Fumitaka Mizoguchi, Gerald F.M. Watts, Michael F. Gurish, Michael B. Brenner, Soumya Raychaudhuri

PNAS 2020. https://doi.org/10.1073/pnas.1912702117

The preprint is available at bioRxiv: https://doi.org/10.1101/571315

Get the code

This repository includes the code for all of the analyses, and it also includes a stand-alone HTML and Javascript data viewer.

Look for the Jupyter notebook files in the analysis folder to see how I ran the analyses.

All the files needed to run the data viewer are in the website folder.

💾 Get the data

All of the RNA-seq and microarray gene expression data is available at NCBI GEO:

• GSE129488

Experimental data (QPCR, ChIP-PCR, ELISA, Migration) is availabe in the experiments.xlsx file.