Navigate to the DataRendering
directory
In the DataRendering
directory:
python3 download_devmouse_grid_gene_expression.py
Downloads energy.raw
files to Data/API/GridData
.
You can use DownloadGridAnnotations
to download the grid annotation data from the current mouse annotation release.
This saves .zip
files to Data/API/AnnotationData
, which you must then manually extract.
Manually download Supplemental Table S4, S5 and S6 from the Cahoy paper "A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function" and save them to Data/Others
.
Rename Supplemental Table S4, S5 and S6 to Astrocyte_Cahoy_S4.xls
, Oligodendrocyte_Cahoy_S5.xls
, and Neuron_Cahoy_S6.xls
, respectively.
Developing mouse gene entrez ID:
- Download the csv from the following: http://api.brain-map.org/api/v2/data/query.csv?criteria=model::Gene,rma::criteria,products[abbreviation$eq%27Mouse%27],rma::options,[tabular$eq%27genes.entrez_id+as+entrez_gene_id%27],[order$eq%27genes.entrez_id%27]&num_rows=all&start_row=0
- Manually delete the first row
- Rename the file to "Adult_geneEntrez" and save it in "Data/API/Genes"
Developing mouse gene abbreviation:
- Download the csv from the following: http://api.brain-map.org/api/v2/data/query.csv?criteria=model::Gene,rma::criteria,products[abbreviation$eq%27DevMouse%27],rma::options,[tabular$eq%27genes.acronym+as+gene_symbol%27],[order$eq%27genes.entrez_id%27]&num_rows=all&start_row=0
- Manually delete row 2108 first
- Then manually delete the first row
- Rename the file to "Dev_geneAbbreviation" and save it in "Data/API/Genes"
Adult mouse gene entrez ID:
- Download the csv from the following: http://api.brain-map.org/api/v2/data/query.csv?criteria=model::Gene,rma::criteria,products[abbreviation$eq%27Mouse%27],rma::options,[tabular$eq%27genes.entrez_id+as+entrez_gene_id%27],[order$eq%27genes.entrez_id%27]&num_rows=all&start_row=0
- Manually delete the first row
- Rename the file to "Adult_geneEntrez" and save it in "Data/API/Genes"
Adult mouse gene abbreviation:
- Download the csv from the following: http://api.brain-map.org/api/v2/data/query.csv?criteria=model::Gene,rma::criteria,products[abbreviation$eq%27Mouse%27],rma::options,[tabular$eq%27genes.acronym+as+gene_symbol%27],[order$eq%27genes.entrez_id%27]&num_rows=all&start_row=0
- Manually delete the rows after 19470 (i.e. starting from row 19471) first
- Then manually delete the first row
- Rename the file to "Adult_geneAbbreviation" and save it in "Data/API/Genes"
In the DataRendering
directory:
python3 getBrainDivision.py
Retrieves the structure information, and descendant structure IDs of each primary structure:
- forebrain (
F
) - midbrain (
M
) - hindbrain (
H
) - dorsal pallidum (
DPall
) - spinal cord (
SpC
)
And saves .csv
files to Data/API/Structures
.
renderBaseData()
Creates processed Matlab data files from raw data for further analysis.
This includes:
makeAnnotationGrids
: annotation of each grid (toannotationGrids.mat
)makeBrainDivision
: (tobrainDivision.mat
) contains IDs of brain subdivisions (forebrain, midbrain, hindbrain, Dpallidum, SpinalCord).energyGrids_*.mat
: voxel-level expression energy of genes at a certain time point.makeGeneExpressionMatrix
->voxelGeneExpression**_*.mat
: voxel x gene expression matrix for each time point.geneID_gridExpression.mat
: ID of genes included in the expression energy of each time pointgoodGeneSubset.mat
: ID of genes with expression data in over 70% of voxels of all time points
renderData()
Generates the default voxel x gene expression matrix and spatial data (distances and correlation) for whole brain and all cell types.
- The parameters of
renderData
can be filled in to make the voxel x gene expression matrix and spatial data for different brain subdivisions (forebrain, midbrain, hindbrain, DPall) and specific cell types (neuron, astrocytes, oligodendrocytes) - To render all data at once, run
renderDataAll