Open for (neuro)science tutorial: Atlases for development Q&A

Thanks for attending the webinar or viewing the video of the Open for (neuro)science: Atlases for development tutorial, with @jeremyinseattle and @Carol! This webinar demonstrated how to use the Allen Developing Mouse Brain Atlas and Brainspan Atlas of the Developing Human Brain in your research.
Please feel free to chime in here with additional questions or follow-up questions to those asked at the live webinar. You can find the recording of this webinar and information about other webinars in this series here.

Question : Could you please explain more precisely the signification of the heat map (log expression of genes)?

Jeremy Miller: Heat maps are a color scale from 0 to a maximum value (there are multiple options for colors, but you can always look at the color bar to see the scale). Each value (in this case voxel) is assigned a color from this scale based on the expression level of that gene. By default “expression energy” is shown. You can learn more about this in the documentation, but essentially it is a metric summarizing level and density of expression in the voxel.

Question : Hi, in each panel, what are the thumbnail images are they different images of the same section?

Kaitlyn Casimo : I think you’re referring to the strip of thumbnail images at the bottom of each panel, correct? They are slices moving from lateral to medial. If you’ve hit “S” to synchronize across all of the experiments, you would be seeing the same slice location for all experiments.

Question : What is the resolution of transcript detection using your ISH approach? Ie the limits of detection. Thank you!

Carol Thompson: The detection limit of our in situ hybridization is not completely known. Detection is impacted by proteinase K concentration (which removes protein and makes the nucleic acids more accessible), tissue thickness (for penetration of probes), length of probe, background signal (which varies by age) and other things. The method uses a non-linear signal amplification which also means that differences in gene expression detected by this technique are not linear, and there is a narrow dynamic range in which you see gradations of signal.

Question : Do you happen to have a plan to provide gene expression atlas using simultaneous detection of gene expression at the genome-wide scale?

Jeremy Miller : There is no plan to expand the current atlas that Carol is presenting to include the remaining genes in the genome.

Kaitlyn Casimo : But you might find our single-cell RNAseq data from our Allen Cell Types Database to be of interest! Note that this only includes data from the adult mouse.

Carol Thompson : And as I mentioned in the talk, there are other large datasets being generated in the community to do single cell profiling across development in human and mouse brain!

Question : Are the strip of thumbnail images always from lateral to medial view?

Carol Thompson : For developing mouse, sagittal data is shown with thumbnails from lateral to medial. For coronal data, it is shown from anterior to posterior.

Question : Is there a reason why the ISH data for the developing human brain vs the other portal (neurotransmitter study, cortex study etc) are not linked? For example, searching the development portal does not find cases that are in the other portal.

Jeremy Miller (live): The datasets were generated at different times through different projects, so they were loaded into the database backend of the website separately. It’s just a practical reason.

Question : Do you need a license to use Allen Brain atlases? What limitations are there if you don’t have a license?

Kaitlyn Casimo : No, you do not need to request a license! The citation policy and terms of use will cover everything you need to know.

Question : How do we download the data?

Kaitlyn Casimo : You can download the data you’re viewing on any page by using the download link at the bottom. You can also download the data through our API: instructions here. For the Brainspan data, there is also a bulk download link in the header of the database home page.

Question : Thanks! Experiment Detail :: Allen Brain Atlas: Human Brain, the strip of images at the bottom. Where can I find this information on your site?

Jeremy Miller: The strip of images at the bottom of the page correspond to all images from a given experiment, which are multiple sections from the same block of tissue. You can access these images in two ways. The first is by clicking the button in the upper right to pop out the image into a new window. Once you do this, you will see a window with a side by side view of the ISH and an annotated Nissl. You can then download individual images from this window using the button on the top with a down arrow. You can also download the data in bulk using our API: instructions here.

Question : Could we search for human brain expression (cell types, regions) with a list of genes not in the vocabulary of your website? what is the limit of the list of genes? thanks

Carol Thompson : Gene searches: Generally our system recognizes the major synonyms of the genes as noted at NCBI. Use an NCBI Entrez gene id or the official gene symbol at NCBI Entrez just to be sure. You can also use an asterisk for a wildcard search, such as “wnt*” to get all wnt genes, or genes that have wnt in the name.

Question : How does Allen’s brain atlases compare to Spatial Genomics?

Carol Thompson : “Spatial transcriptomics” is a method to use a combinatorial code to probe 10s of genes at a time in the same section of tissue. Examples of spatial transcriptomics methods is MERFISH (multiplexed error-robust fluorescence in situ hybridization) or osmFISH (cyclic-ouroboros smFISH). These methods are quite new and likely represent the next evolution in comprehensive spatial characterization of gene expression. Analysis methods for these types of data are still evolving, and our Allen Brain Atlas ISH data will likely serve as a good reference control for laboratories seeking to validate their new spatial transcriptomic protocols.