This respository contains all of the code used to analyze snRNA-seq data from the study Molecular states underlying neuronal cell type development and plasticity in the whisker cortex. All of the outputs have been cleared to make the files <25MB for GitHub upload. Notebooks with full outputs can be found here: https://drive.google.com/drive/folders/1-mZdY1pc3NT2rcrwFW3I-bH6lykzn0KU?usp=sharing
All of the finalized datasets associated with the study can be found here: https://drive.google.com/drive/folders/1xcCARVoPE9cPhbTT8ko7rz-RKfE07X-q?usp=sharing. Note that these h5ad files contain normalized, log-transformed data as described in the manuscript. If you are interested in raw counts, see the folder "Raw_Counts_Samples" at the above link.
Note that some sample names are different between the data and paper. Here are the 1:1 mappings: ['A1', 'A2', 'B2', 'C1', 'C2', 'D1', 'D2', 'D2new', 'D3', 'S1', 'S2', 'S3'] in the data = ['A1', 'A2', 'S4', 'C1', 'C2', 'D1', 'D2', 'D4', 'D3', 'S1', 'S2','S3'] in the paper.
.bam files for each sample generated in the study can be found at NCBI GEO GSE276528.
Please contact salwan@berkeley.edu and kshekhar@berkeley.edu with any questions.