The spatial landscape of gene expression isoforms in tissue sections

<p><strong>This upload&nbsp;provides raw in situ sequencing (ISS) data used to validate Spatial Isoform&nbsp;Transcriptomics (SiT), as well as&nbsp;R scripts required for SiT analysis.</strong></p> <p><strong>GenePlots.zip and Reads.zip are ISS data </strong><strong>generated and collected by the CARTANA ISS service</strong>.&nbsp;<strong>The following data description is cited from the&nbsp;report provided by CARTANA ISS service:</strong></p> <p><em>&quot;Folder &quot;Reads&quot; contains coordinates and gene information of segmented spots.<br> The coordinates are in pixel unit. Scaling factor is 0.32 um/pixel. (0,0) is at northwest (top-left corner).<br> 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.</em></p> <p><em>Files ending with _LowThreshold: reads not matching with any known barcode were already discarded.</em></p> <p><em>Files ending with _HighThreshold: has information only about spots that passed additional quality check.</em></p> <p><em>Folder &quot;GenePlots&quot; has plotted images in static .png format, fully zoomed out. LowThreshold and HighThreshold follow the same thresholding strategy as in reads files.&quot;</em></p> <p>&nbsp;</p> <p><strong>SiT-master.zip is a download of the&nbsp;GitHub repository </strong><a href="https://github.com/ucagenomix/SiT">https://github.com/ucagenomix/SiT</a>,&nbsp;<strong>providing figures and analysis scripts for SiT.</strong></p> <p>&nbsp;</p> <p><strong>Related SiT data are deposited through&nbsp;GEO, accession number&nbsp;<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE153859">GSE153859</a></strong></p>