The spatial landscape of gene expression isoforms in tissue sections

This upload provides raw in situ sequencing (ISS) data used to validate Spatial Isoform Transcriptomics (SiT), as well as R scripts required for SiT analysis.

GenePlots.zip and Reads.zip are ISS data generated and collected by the CARTANA ISS service. The following data description is cited from the report provided by CARTANA ISS service:

"Folder "Reads" contains coordinates and gene information of segmented spots.
The coordinates are in pixel unit. Scaling factor is 0.32 um/pixel. (0,0) is at northwest (top-left corner).
With Low/High Threshold, we refer to the quality thresholding. Our technology is fluorescence based, i.e. with the thresholding one can balance how certain the signals are.

Files ending with _LowThreshold: reads not matching with any known barcode were already discarded.

Files ending with _HighThreshold: has information only about spots that passed additional quality check.

Folder "GenePlots" has plotted images in static .png format, fully zoomed out. LowThreshold and HighThreshold follow the same thresholding strategy as in reads files."

SiT-master.zip is a download of the GitHub repository https://github.com/ucagenomix/SiT, providing figures and analysis scripts for SiT.

Related SiT data are deposited through GEO, accession number GSE153859