Transcriptional profiling of pre- and post-natal glutamatergic progenitors and nascent neurons by single cell RNA sequencing. Transcriptional profiling of pre- and post-natal glutamatergic progenitors and nascent neurons by single cell RNA sequencing

Purpose: We labeled synchronous cohorts of prenatal and postnatal glutamatergic progenitors to study their lineage relationship and transcriptional specificities. Method and results: We performed scRNA-seq of postnatal glutamatergic progenitors isolated from microdissected pallium at E15.5 or dorsal subventricular zone at P2 in the mouse. Our results highlight transcriptional dysregulation at P2 which includes genes involved in metabolism, differentition and migration. Overall design: tdTom+ cells (glutamatergic progenitors) were isolated from E15 and P2 transgenic mice expressing a tamoxifen inducible Cre-recombinase under Neurog2 genomic regulatory sequences. A total of 230 cells were obtained (121 at E15.5 and 109 at P2). Following tissue dissociation, single cells were isolated by flow cytometry and processed with the C1 Single-Cell Auto Prep System (Fluidigm). RNA-sequencing libraries were muliplexed and sequenced at 75bp single reads using the Illumina HiSEQ500 platform at a depth of 7M reads. Every sample in this series represents a single cell.

研究目的：对产前及产后谷氨酸能前体细胞的同步队列进行标记，以探究其谱系关联与转录特异性。
方法与结果：针对小鼠胚胎期15.5天（E15.5）显微切割的端脑皮层，以及产后2天（P2）背侧室管膜下区分离获得的产后谷氨酸能前体细胞，我们开展了单细胞RNA测序（single-cell RNA-sequencing, scRNA-seq）。研究结果显示，P2时期存在转录失调现象，涉及代谢、分化及迁移相关基因。
整体实验设计：我们使用在神经源性分化因子2（Neurog2）基因组调控序列下表达他莫昔芬诱导型Cre重组酶的转基因小鼠，从E15和P2时期的小鼠体内分离得到tdTom+（tdTomato阳性）的谷氨酸能前体细胞。最终共获取230个单细胞（E15.5时期121个，P2时期109个）。组织解离后，通过流式细胞术分离单细胞，并采用C1单细胞自动制备系统（C1 Single-Cell Auto Prep System，Fluidigm公司）进行样本处理。RNA测序文库经多重建库后，利用Illumina HiSEQ500测序平台开展75碱基单端测序，测序深度为700万条读段（7M reads）。本数据集的每一个样本均代表单个单细胞。