This repository contains all the codes and other documents related to the manuscript Kuehn et al 2021.
R CODES and ASSOCIATED SPREADSHEETS
R codes for all three analyses below are in the "analysis.rmd" file. (The bootstrap is running with 10,000 iterations right now, which will probably take a while (maybe 5-10 minutes) if you just run the code, so if you want to run the code faster, just set nboot (on line 64) to a smaller number.)
- Dataset 01: Vasa cluster analysis in control worms
- Dataset 02: Low and High density culturing experiment analyis
- Dataset 03: P10-P20 amputation experiment analysis
IMAGE ANALYSIS FILES
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Low and High density culturing experiment scoring: https://doi.org/10.5281/zenodo.4587817
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P10-P20 amputation experiment scoring: https://doi.org/10.5281/zenodo.4587804
HCR PROBE GENERATOR
This program written by Ryan Null allows you ease of ordering probes that mesh with the published HCR system of reaction and amplification reagents. https://github.com/rwnull/insitu_probe_generator
PROTOCOLS
- Özpolat Lab fixation protocol
- Özpolat Lab in situ hybridization protocol
- Özpolat Lab HCR protocol (with Bria Metzger and Dr. Ryan Null's changes to the original Choi et al 2018 protocol)