PT  - JOURNAL ARTICLE
AU  - Stickels, Robert R.
AU  - Murray, Evan
AU  - Kumar, Pawan
AU  - Li, Jilong
AU  - Marshall, Jamie L.
AU  - Di Bella, Daniela
AU  - Arlotta, Paola
AU  - Macosko, Evan Z.
AU  - Chen, Fei
TI  - Sensitive spatial genome wide expression profiling at cellular resolution
AID  - 10.1101/2020.03.12.989806
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.03.12.989806
4099  - http://biorxiv.org/content/early/2020/03/14/2020.03.12.989806.short
4100  - http://biorxiv.org/content/early/2020/03/14/2020.03.12.989806.full
AB  - The precise spatial localization of molecular signals within tissues richly informs the mechanisms of tissue formation and function. Previously, we developed Slide-seq, a technology which enables transcriptome-wide measurements with 10-micron spatial resolution. Here, we report new modifications to Slide-seq library generation, bead synthesis, and array indexing that markedly improve the mRNA capture sensitivity of the technology, approaching the efficiency of droplet-based single-cell RNAseq techniques. We demonstrate how this modified protocol, which we have termed Slide-seqV2, can be used effectively in biological contexts where high detection sensitivity is important. First, we deploy Slide-seqV2 to identify new dendritically localized mRNAs in the mouse hippocampus. Second, we integrate the spatial information of Slide-seq data with single-cell trajectory analysis tools to characterize the spatiotemporal development of the mouse neocortex. The combination of near-cellular resolution and high transcript detection will enable broad utility of Slide-seq across many experimental contexts.