**We would like to access the .csv file containing the ISH data for the mouse Sleep study (Sleep Study :: Allen Brain Atlas: Mouse Brain), but have not been able to access it through the API. Is there a step-by-step way to do this, or is there even access to the data? We would like to download expression values for different genes in all brain regions studied in a .csv format and then use R for analysis of these data. We’d like to be able to complete the data analysis by the end of the month (August 2021). We plan on using this data for a case study in September that will be implemented in 5 classes at two different institutions (>400 students).
Hi @sabrine ,
Unfortunately, there is no single csv file that contains all the ISH expression data for this study. Expression values for individual experiments can be downloaded using the instructions for the Adult Mouse Brain Atlas: API - Allen Mouse Brain Atlas
For example, you can download a binary file of expression per voxel with a command like http://api.brain-map.org/grid_data/download/77348165 (Gene Arr3 for condition RS-C,sagittal).
Or you can download expression values summarized by each structure for that experiment with http://api.brain-map.org/api/v2/data/SectionDataSet/query.json?id=77348165&include=structure_unionizes(structure) .
A list of all genes in the Sleep Study can be obtained with: https://api.brain-map.org/api/v2/data/Gene/query.json?criteria=products[id$eq15]
All experiments for the Sleep Study can be obtained with https://api.brain-map.org/api/v2/data/SectionDataSet/query.json?criteria=products[id$eq15]&include=genes