Transcriptome-wide spatial RNA profiling maps the cellular architecture of the developing human neocortex
Transcriptome-wide spatial RNA profiling maps the cellular architecture of the developing human neocortex
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DOI：
10.1101/2021.03.20.436265
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发表时间：
2021-03
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通讯作者：
Kenny Roberts;Alexander Aivazidis;Vitalii Kleshchevnikov;Tong Li;Robin Fropf;M. Rhodes;J. Beechem;M. Hemberg;O. Bayraktar
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文献类型：
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作者：
Kenny Roberts;Alexander Aivazidis;Vitalii Kleshchevnikov;Tong Li;Robin Fropf;M. Rhodes;J. Beechem;M. Hemberg;O. Bayraktar
空间基因组技术可以映射组织中的基因表达，但提供有限的潜力，转录组范围内的发现方法和应用于固定的组织样品。在这里，我们介绍GeoMX全转录组图谱（WTA），一种新的技术，用于组织的转录组范围的空间分析与细胞分辨率。WTA显著扩展了数字空间分析方法，使用测序读数以高通量对18，190个基因进行原位杂交。我们应用WTA生成了人类胎儿新皮层的第一个空间转录组图谱，验证了福尔马林固定组织材料上的转录组空间分布，并证明了自闭症基因表达在深层皮层中的空间富集。为了证明WTA对细胞图谱的价值，我们整合了单细胞RNA测序（scRNA-seq）和WTA数据，以空间映射数十种神经细胞类型，并表明WTA可用于直接原位测量细胞类型特异性转录组。此外，我们开发了用于WTA数据的背景校正和与scRNA-seq的准确整合的计算工具。我们的研究结果表明，WTA是一种通用的全转录组发现工具，用于细胞图谱和固定组织空间转录组学。
Spatial genomic technologies can map gene expression in tissues, but provide limited potential for transcriptome-wide discovery approaches and application to fixed tissue samples. Here, we introduce the GeoMX Whole Transcriptome Atlas (WTA), a new technology for transcriptome-wide spatial profiling of tissues with cellular resolution. WTA significantly expands the Digital Spatial Profiling approach to enable in situ hybridisation against 18,190 genes at high-throughput using a sequencing readout. We applied WTA to generate the first spatial transcriptomic map of the fetal human neocortex, validating transcriptome-wide spatial profiling on formalin-fixed tissue material and demonstrating the spatial enrichment of autism gene expression in deep cortical layers. To demonstrate the value of WTA for cell atlasing, we integrated single-cell RNA-sequencing (scRNA-seq) and WTA data to spatially map dozens of neural cell types and showed that WTA can be used to directly measure cell type specific transcriptomes in situ. Moreover, we developed computational tools for background correction of WTA data and accurate integration with scRNA-seq. Our results present WTA as a versatile transcriptome-wide discovery tool for cell atlasing and fixed tissue spatial transcriptomics.