PRJNA675891: Next Generation Sequencing Analysis of Transcriptomes in maculopapular drug rash with COVID-19 infection

概要: Next Generation Sequencing Analysis of Transcriptomes in maculopapular drug rash with COVID-19 infection

项目整体设计: Purpose: Investigate whether maculopapular drug rash with COVID-19 infection (COVID19-MDR) exhibits a distinct gene expression in the skin as compared to non-COVID19-MDR. Methods:RNA was extracted from formalin-fixed, paraffin-embedded (FFPE) skin biopsies from COVID-MDR (n=3), MDR (n=7), and Healthy control (n=5). Library preparation for RNA-seq was performed by using the TruSeq Stranded RNA library preparation kit including polyA enrichment (Illumina) from total RNA. Sequencing was performed on the the Illumina NextSeq 500 platform with 75 cycles. Results: RNA sequencing from lesional skin showed that pathways of cytolysis and eosinophil chemotaxis were activated in COVID MDR. Cytolysis/cellular defense response related genes, such as PRF1 (perforin), GZMA (Granzyme A) and GNLY (Granulysin), as well as eosinophil migration/lymphocyte chemotaxis genes, e.g. C-C Motif chemokine ligand 5 (CCL5), CCL13, were upregulated in COVID MDR. Conclusions: This study provide an opportunity to understand the pathogenesis of MDR with the COVID-19 infection. We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.