The spatial landscape of gene expression isoforms in tissue sections
Authors/Creators
- 1. Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, F06560 Sophia Antipolis, France
- 2. Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
- 3. Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
Description
This upload provides raw in situ sequencing (ISS) image data used to validate Spatial Isoform Transcriptomics (SiT). The data were 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."
Related SiT data are deposited through GEO, accession number GSE153859
Files
GenePlots.zip
Files
(28.5 MB)
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Additional details
Related works
- Is supplement to
- Preprint: 10.1101/2020.08.24.252296 (DOI)