TIRAP drives myelosuppression through an Ifn?-Hmgb1 axis that disrupts the endothelial niche.

Purpose: The goals of this study are to compare the transcriptome profile of mouse hematopoietic stem/progenitor cells (HSPC) from the bone marrow overexpressing the innate immune adaptor protein TIRAP to control vector expressing HSPC using RNA-Seq. Methods: mRNA profiles of wild-type (WT) mice bone marrow overexpressing TIRAP or control vectors were generated by deep sequencing, in triplicate, using the Illumina platform. RNA-Seq data were aligned using JAGuaR (v2.0.3), using the mm10 reference. Expression quantification was performed with Sailfish (v0.6.2), using RefSeq gene models. The differential expression analysis between TIRAP expressing bone marrow and control was performed using DESeq2 (v1.10.1). Results: Using an optimized data analysis workflow, we mapped approximately 92% sequenced reads on average per sample to the mouse genome (build mm10). Overall design: Bone marrow mRNA profiles of wild type (WT) mice overexpressing either TIRAP or control (MIG) vectors.

本研究旨在通过RNA测序（RNA-Seq），比较过表达先天免疫适配蛋白TIRAP的小鼠骨髓造血干/祖细胞（hematopoietic stem/progenitor cells, HSPC）与转染对照载体的HSPC的转录组谱。
方法：采用Illumina测序平台，对过表达TIRAP或对照载体的野生型（wild-type, WT）小鼠骨髓样本的mRNA谱进行三次生物学重复的深度测序。RNA测序（RNA-Seq）数据通过JAGuaR（v2.0.3）以mm10参考基因组进行序列比对；表达定量分析采用Sailfish（v0.6.2），基于RefSeq基因模型完成。TIRAP过表达骨髓样本与对照样本间的差异表达分析采用DESeq2（v1.10.1）完成。
结果：通过优化的数据分析流程，我们将每个样本平均约92%的测序读段比对至小鼠基因组（构建版本mm10）。
实验设计：野生型小鼠骨髓的mRNA谱分别来自过表达TIRAP载体或对照（MIG）载体的样本。