Upf2_migration_2026

This repository contains the data analysis code used in the manuscript:

Nonsense-mediated mRNA decay orchestrates neuronal migration and cortical lamination while modulating reelin and ciliary gene regulatory networks
Lin Lin^#, Naoto Kubota^#, Yi-Li Lam, Michelle Mingxue Song, Min Zhang, Sika Zheng. (^#Equal contribution)
Cell reports 2026.

Dependencies

Snakemake pipeline

• preprocessing_RNAseq.smk and kb-nac.smk in SnakeNgs (v0.2.0)
• preprocessing_ChIPseq.smk in SnakeNgs (v0.3.2)
• SnakeShiba in Shiba (v0.4.0)

Docker image

• naotokubota/my_notebook:1.6.3
• naotokubota/scanpy_jupyter:1.3.9
• naotokubota/scanpy_jupyter:stream-0.1