Atlas_Normal

• [24.03.27] Version 5 (Final): All minor updates in data (Brain region, cluster order, etc.) has been resolved.
• [24.03.02] Version 4: Cluster resolution and annotation has been refined, especially for neuroblasts.
• [23.12.17] Version 3: Age of Braun-derived data was corrected from a notation based on weeks to days.

Multipanel Automation (Run in Linux environment)

1. Clone this repository:

git clone https://github.com/joonan-lab/Atlas_Normal

2. Create a conda environment using the provided YAML file and activate it:

conda env create --file BrainAtlas.yaml
conda activate BrainAtlas

3. Install the required packages:

sudo apt-get update
sudo apt-get install libmagick++-dev
sudo apt-get install libpoppler-cpp-dev

4. Execute the following code:

python Automation_v5.py {dir/to/adata_file} {dir/to/psbulk_file} {target_gene1} {target_gene2} {target_gene3} ...

• adata_file: Output_240611_adata_scvi_random_sampleID.h5ad (Minor changes made to the color palette for brain regions compared to the 240327 dataset)
• psbulk_file: Pseudobulk_mincells_30_lognorm_mean_0327.h5ad

References.

• Braun, E., et al. (2023). Comprehensive cell atlas of the first-trimester developing human brain. Science, DOI: 10.1126/science.adf1226 (EGAS00001004107)
• Cameron, D., et al. (2023). Single-Nuclei RNA Sequencing of 5 Regions of the Human Prenatal Brain Implicates Developing Neuron Populations in Genetic Risk for Schizophrenia. Biological Psychiatry, DOI: 10.1016/j.biopsych.2022.06.033 (EGAS00001006537)
• Hardwick, SA., et al. (2022). Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. Nature Biotechnology, DOI: 10.1038/s41587-022-01231-3 (GSE178175)
• Herring, CA., et al. (2022). Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution. Cell, DOI: 10.1016/j.cell.2022.09.039 (GSE168408)
• Morabito, S., et al. (2021). Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s disease. Nature Genetics, DOI: 10.1038/s41588-021-00894-z (GSE174367)
• Nagy, C., et al. (2020). Single-nucleus transcriptomics of the prefrontal cortex in major depressive disorder implicates oligodendrocyte precursor cells and excitatory neurons, Nature Neuroscience, DOI: 10.1038/s41593-020-0621-y (GSE144136)
• Human M1 10x, Allen Brain Map (https://portal.brain-map.org/atlases-and-data/rnaseq/human-m1-10x)
• Single-cell transcriptomic and proteomic analysis of Parkinson’s disease brains, Human Cell Atlas (https://data.humancellatlas.org/explore/projects/9a23ac2d-93dd-4bac-9bb8-040e6426db9d)