Li, Zhenyu

Project: Transcriptome analysis of macrophages and platelets in inflammation

Macrophages and platelets are important players in diseases involving inflammation. Many studies have shown that gene expression in the two cell types have profound impact on the progression and resolving of inflammation. However, most studies examine a subset of genes at one time, which is a very limited view of the landscape of gene regulation at transcription level. By looking at transcriptome using RNA-seq and single-cell RNA-seq, our lab study how changes in gene expression determine the cellular functions and the interaction between macrophages and platelets. Using HPC, we calculate lab-produced and public RNA-Seq datasets. Because of the size of the datasets of sequence reads, we need use of high performance computing capacity. Single-cell RNA-seq is still in its infancy, we will need to test and evaluate newly developed open source tools as they become available.

Computational Method:

Open source UNIX-based RNA-seq and single-cell RNA-seq data analyzing tools.

Software:

RNA-seq data analysis pipeline: STAR, HISAT2, Magic-BLAST, bowtie2, salmon, kallisto, stringtie, DEseq, edgeR, Trinity, RSEM, HTseq-count, featureCount

Personnel involved in project and use of HPC:

Congqing Wu, Postdoctoral scholar

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