This study corresponds to the paper:

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

Stickels, Murray, et al. Nat. Biotech 2020.

This repository was formerly called:

"Sensitive spatial genome wide expression profiling at cellular resolution."

Stickels, Murray et al., Biorxiv 2020.

Abstract: 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.

Data Download: Data supporting the findings above is available for download through this study, produced in the labs of Fei Chen and Evan Macosko. For each Slide-seqV2 puck used, we have provided a raw counts digital gene expression (DGE) matrix (.txt.gz) and a bead barcode locations file (.csv). The pucks are used throughout figures and analyses as follows.

We also include the bam files for each of the pucks from this study as well under the download tab

 * NOTE: Pucks labeled as Slide-seq were performed in accordance with the previous version of the technology. All other pucks are performed with the Slide-seqV2 protocol. 

FigurePuck Used (Tissue Type)
1APuck_200115_08 (mouse hippocampus)
1BPuck_190926_03 (mouse embryo), Puck_191007_07 (mouse embryo Slide-seq)
1C/DPuck_200115_08 (mouse hippocampus)
2Puck_191204_01 (mouse hippocampus), Puck_191219_17 (mouse hippocampus), Puck_191219_18 (mouse hippocampus), Puck_191219_20 (mouse hippocampus)
3Puck_190921_19* (mouse E15 brain)
S3Puck_200115_08 (mouse hippocampus), visium data is coronal section from 10x website, Puck_200127_15 (mouse olfactory bulb), HDST data is from published data
S4Puck_200306_03 (mouse somatosensory cortex)
S5Puck_200115_08 (S5A-B, mouse hippocampus), Puck_200306_03, Puck_200306_02 (S5C, mouse somatosensory cortex)
S6Puck_191204_01 (mouse hippocampus), Puck_191219_17 (mouse hippocampus), Puck_191219_18 (mouse hippocampus), Puck_191219_20 (mouse hippocampus)
S7Puck_190921_19* (mouse E15 brain), Puck_190926_03 (E12.5 mouse embryo)
S8Puck_190921_19* (mouse E15 brain) , Puck_190926_03 (E12.5 mouse embryo)
Supplementary Table 7Puck_190926_01, Puck_190926_02, Puck_190926_03, Puck_190926_06