Shared Data/Tools

ZipSeq Reagent Setup and QC rev B: This short guide will take you through the best practices I've found for generating the oligo-Ab conjugates described in our Nat. Methods paper and how to QC them on test cells w/ flow cytometry. It also lays out how to test hybridization of strands and photouncaging 'binariness'
ZipSeq Sectioning version1: This short guide takes you through how to section your tissue well which is critical for the zipseq method. This document is performed on lymph nodes as an example, but works with PyMT tumors as well.
After a hiatus, please find the first version of the sample mounting, imaging, region selection, automated illumination and zipcode addition steps here: ZipSeq Sample Mounting, Imaging and barcoding-Rev A
ZipSeq Library Construction RevB: This will take you through the library construction steps for the zipcodes and recommended sequencing parameters as well as troubleshooting for common issues during the zipcode amplification steps. (Note, there was an error in RevA in the cycling protocol. This has been updated.)
Visual Basics Plugin (by John Eichorst) for automated ROI generation across multiple FOV for Mosaic targeted illumination through Metamorph: https://github.com/BIDCatUCSF/VB-Plugin-for-Patterned-Illumination

Code used for analysis in "Spatiotemporal co-dependency between macrophages and exhausted CD8 ⁺ T cells in cancer" can be found here: https://github.com/ken7hu/ZipSeq-Analysis-CD206R
Lab Plasmids at Addgene

Microscopy Related

Building a 2-Photon Microscope

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