Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain

Description of files in repository

Contains the source code for data analysis performed for Lange et al., 2019. The sequencing data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE137525 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137525). For a description of the computational methods please see Lange et al., 2019.

• envrionement.yml: anaconda environment for executing zebrafish_neurogenesis_smartseq_prepare_data.R and zebrafish_neurogenesis_smartseq_manuscript.ipynb
• zebrafish_neurogenesis_smartseq_prepare_data.R: reading the count data, calculation of quality metrics
• zebrafish_neurogenesis_smartseq.h5ad the prepared count data whcih can be read using scanpy and is used to start the actual analysis in zebrafish_neurogenesis_smartseq_manuscript.ipynb
• zebrafish_neurogenesis_smartseq_manuscript.ipynb: contains all the analysis of the single-cell seq data except for the cell type homology analysis
• environment_2.yml: anaconda environment for executing Hochgerner_2018.ipynb
• mart_export.txt: the list of orthogolous genes used for the cell type homology analysis
• Hochgerner_2018.ipynb: contains the cell type homology analysis

Citation

Lange C, Rost F, Machate A, Reinhardt S, Lesche M, Weber A, Kuscha V, Dahl A, Rulands S, Brand M. Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain, under review