Data analysis workflow
GWAS-eQTL colocalization analysis workflow by Fang Li
RNA-seq data analysis workflow by Hanrui
Pathway and network analysis workflow by Hanrui
Functional genomic tools and fundamentals(HTML) by Jianting
Single cell RNA-seq analysis using Seurat 2.3.4 (Rmd)/(HTML), Seurat 3.0 (Rmd), and Seurat 3.1 (Rmd)/(HTML) by Sophie and Hanrui
We published the protocol to differentiate human induced pluripotent stem cell (iPSC) to macrophages. iPSC-derived macrophages (IPSDM) obtained using this protocol have demonstrated excellent functional and transcriptomic fidelity relative to human monocyte-derived macrophages (HMDM), with advantages and successful applications in disease modeling using patients-derived and CRISPR-edited iPSC lines (ATVB 2017). Through deep RNA-sequencing, the coding transcriptome (Circ Res 2015), alternative splicing events (ATVB 2016) and long non-coding RNA profiles (JAHA 2017) between isogenic IPSDM and HMDM at baseline and during activation are characterized, providing a comprehensive resource for planning IPSDM studies to model such events. This protocol and the associated resources provide a unique platform to understand human macrophage-specific functional, transcriptomic and genomic features in physiology and a broad spectrum of macrophage-relevant diseases.
The RNA-seq data of isogenic IPSDM and HMDM can be visualized in the UCSC genome browser by adding track hub using URL https://de.cyverse.org/anon-files/iplant/home/chenyix/trackhub/GENEiPS_scaled/hub.txt or through the following link. The original RNA-seq data are available from the NCBI Gene Expression Omnibus (GEO) under the accession number GSE55536.
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