Transcriptomic changes induced in one cell type by another mediate many biological processes in the brain and elsewhere; however, achieving artifact-free physical separation of cell types to study them is challenging and generally allows for analysis of only a single cell type. We describe an approach using a co-culture of distinct cell types from different species that enables physical cell sorting to be replaced by in silico RNA sequencing (RNA-seq) read sorting, which is possible because of evolutionary divergence of messenger RNA (mRNA) sequences. As an exemplary experiment, we describe the co-culture of purified neurons, astrocytes, and microglia from different species (12-14 d). We describe how to use our Python tool, Sargasso, to separate the reads from conventional RNA-seq according to species and to eliminate any artifacts borne of imperfect genome annotation (10 h). We show how this procedure, which requires no special skills beyond those that might normally be expected of wet lab and bioinformatics researchers, enables the simultaneous transcriptomic profiling of different cell types, revealing the distinct influence of microglia on astrocytic and neuronal transcriptomes under inflammatory conditions.

中文翻译：

---

混合物种RNA-seq，用于阐明基因转录的非细胞自主控制。

一种细胞类型由另一种细胞诱导的转录组变化介导了大脑和其他地方的许多生物学过程。然而，实现细胞类型的无伪造物物理分离以研究它们是具有挑战性的，并且通常只允许分析单个细胞类型。我们描述了一种使用不同物种的不同细胞类型进行共培养的方法，该方法使物理细胞分选可以被计算机RNA测序（RNA-seq）读取分选所取代，这可能是由于信使RNA（mRNA）的进化差异所致序列。作为一个示例性实验，我们描述了来自不同物种（12-14天）的纯化神经元，星形胶质细胞和小胶质细胞的共培养。我们描述了如何使用Python工具Sargasso，可以根据物种从常规RNA-seq中分离出读段，并消除不完整的基因组注释所带来的任何假象（10小时）。我们展示了该程序如何不需要湿实验室和生物信息学研究人员通常期望的特殊技能，就能实现不同细胞类型的同时转录组分析，揭示小胶质细胞在炎性条件下对星形胶质细胞和神经元转录组的独特影响。