BARseq2 in M1 and A1

Published: 08-04-2021| Version 2 | DOI: 10.17632/jnx89bmv4s.2
Shaina Lu,
Jesse Gillis,
Anthony Zador


BARseq2 in M1 and A1. Including processed projection data, in situ sequencing data, and analysis scripts. Also include helper files needed to run the scripts. Accompanying Sun et al., 2021 Nat Neurosci


Steps to reproduce

Add helpers to MATLAB path. For gene-only datasets, run "Gene-only analysis/GeneExpressionAnalysis-newtyping.ipynb". For gene-projection datasets, run "Gene-projection analysis/barseqanalysis-singleprojectionsonly-newthresh.ipynb". Processed data needed to run these scripts are provided in the respective folders. These data were produced using scripts in "scrtips for processing raw images" in each folder, using raw image data deposited at Brain Image Library For the CTB validation experiment, intermediate data after quantification is provided with scripts to consolidate results from different experiments. For the marker_panel_performance and cadherin_coexp_module, the raw data needed to reproduce figures are from Tasic et al 2018 and Yao et al 2020. Version 2 included helper files to design padlock probes, and a sample script used to design probes for marker genes in MOp. These scripts require a locally installed Blast+, which can be downloaded from NCBI.