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human_developing_spinal_cord.

Citation

This is a public repository containing scripts used in the publication:

Li X et al. Decoding spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin

Nature Neuroscience 2023 (https://www.nature.com/articles/s41593-023-01312-9)

Running the analysis

The analysis scripts are available in the code folder and is empty by default. The data folder is used to host the raw counts and other files used for the analysis. Some datasets require manual download and should be placed in the corresponding folder. The results folder, also empty by default, will store the output from analysis performed. The analysis done herein can be reproduced by installing CONDA and running:

  1. Clone this repository\
git clone https://github.com/czarnewski/human_developing_spinal_cord.git
  1. Create and activate the conda environment\
cd human_developing_spinal_cord

conda activate base
conda install -c conda-forge mamba

mamba env create -n dev_sc -f env_dev_sc.yml
conda activate dev_sc

Datasets

The list of all datasets used in the manuscript are depicted below:

Technology Dataset source publication Accession no
10X scRNAseq Human developing spinal cord this manuscript GSE219122
10X Visium Human developing spinal cord this manuscript GSE219122
10X scRNAseq Mouse adult spinal cord [Sathyamurthy et al. 2018 Cell Rep] (https://pubmed.ncbi.nlm.nih.gov/29466745/) GSE103892
10X scRNAseq Mouse juvenile spinal cord [Zeisel et al. 2018 Cell] (https://pubmed.ncbi.nlm.nih.gov/30096314/) SRP135960
SplitSeq Mouse postnatal [Rosenberg et al. 2018 Science] (https://pubmed.ncbi.nlm.nih.gov/29545511/) GSE110823
10X scRNAseq Mouse adult spinal cord Blum et al. 2021 Nat Neurosci GSE161621
10X scRNAseq Mouse adult spinal cord Alkaslasi et al. 2021 Nat Comm GSE167597
10X scRNAseq Mouse developing spinal cord Delile et al 2019 Development E-MTAB-7320
10X scRNAseq Human developing spinal cord Rayon et al 2021 Development GSE171892
10X scRNAseq Mouse juvenile spinal cord Milich et al 2021 J Exp Med GSE162610
10X scRNAseq Human developing spinal cord Zhang et al 2021 EMBO Rep GSE136719
10X scRNAseq Human ependymomas Gojo et al 2020 Cancer Cell GSE136719