Hello, I have some questions regarding this field as I am new to it. I have single-cell sequencing data from a brain organoid, and I would like to compare the transcriptional similarity with the spinal cord data from the Allen Brain human brain microarray dataset, as shown in Figure 1. However, I am not sure which data to download. Does the Allen Brain Atlas (ABA) provide single-cell sequencing data for specific regions, such as the human medulla? Additionally, I am not quite clear on how to analyze the microarray data. Is there any relevant introduction or guidance available? Thank you very much for your response.
Can you please clarify exactly what you are looking to do so we can better assist you? You’ve mentioned a lot of largely unrelated topics, and referenced a figure that isn’t included. Thanks.
Sorry for some confusion. Does the Allen Brain Atlas (ABA) provide single-cell sequencing data for specific regions, such as the human medulla? Thank you for your patience and guidance.
Got it, and yes. As part of the Allen Brain Cell (ABC) Atlas, we provide data, a GUI tool for interactive with data, and some Jupyter notebooks for access of single cell data spanning the whole human and whole mouse brain. For human, the anatomic specificity is at the level of microdissection, while for mouse there is accompanying MERFISH data and associated brain region annotations to provide cell-level resolution.