RNA-seq of laser-capture microdissected 50x50x50 um tissue cubes from the medial ganglionic eminence of wild-type and GFRa1 mutant mice

Cortical interneurons originating from the medial ganglionic eminence (MGE) are among the most diverse cells within the CNS. Different pools of proliferating progenitor cells are thought to exist in the ventricular zone of the MGE, but whether the underlying subventricular and mantle regions of the MGE are spatially patterned has not yet been addressed. Here, we combined laser-capture microdissection and multiplex RNA-sequencing to map the transcriptome of MGE cells at a spatial resolution of 50 µm. Distinct groups of progenitor cells showing different stages of interneuron maturation were identified and topographically mapped based on their genome-wide transcriptional pattern. One 50 µm coronal section from the MGE was taken from each of two wildtype and one GFRa1 mutant E12.5 C57bl6/J mouse. Each section was laser microdissected into approximately 100 cubes, covering the whole MGE, and each cube was further processed for RNA-seq analysis.起源于内侧神经节隆起（medial ganglionic eminence, MGE）的皮层中间神经元，是中枢神经系统（Central Nervous System, CNS）中种类最为多样的细胞类群之一。此前研究认为内侧神经节隆起的脑室区存在多群增殖性祖细胞，但内侧神经节隆起下方的室下区与套层是否存在空间模式化分布，迄今尚未得到阐明。本研究结合激光捕获显微切割（laser-capture microdissection）与多重RNA测序（multiplex RNA-sequencing）技术，以50微米的空间分辨率对内侧神经节隆起细胞的转录组进行了图谱绘制。本研究基于全基因组转录特征，鉴定出了呈现中间神经元成熟不同阶段的多组独特祖细胞，并对其进行了空间定位绘图。本研究从2只野生型及1只GFRα1突变型胚胎期12.5天（E12.5）的C57BL/6J小鼠中，各取材获取一块内侧神经节隆起的50微米冠状切片。每块切片均通过激光显微切割切割为约100个小立方体，完整覆盖整个内侧神经节隆起，随后对每个小立方体分别进行RNA测序分析。