Thank you for attending or viewing the video of "The Virtual Lab: Building Blocks of the Brain” webinar. Please feel free to chime in with additional questions or follow-ups, and to continue the conversation more generally here in this thread. You can find the recording of this webinar and information about upcoming webinars at alleninstitute.org/virtual-lab-webinars.
These were the questions posed in the Q&A during the webinar and answered by me @kaitlync and Luke Esposito @Luke_E.
Question: Do we have any case history about the 6 donors in the human brain atlas? I think I recall it is somewhere in the documentation but can you review that?
Kaitlyn: You can find case history and demographic information for all six subjects in the documentation for the Allen Human Brain Atlas, which you can find by either clicking on the documentation link from any page in that database or here: help.brain-map.org/display/humanbrain/Documentation.
Question: What is the best tool to use with students to help them understand the general roles of different anatomical structures (i.e. Basal ganglia)?
Kaitlyn: That’s a great question. I would suggest using a combination of our reference atlas showing anatomy + the microarray data to show gene expression, and then in the lesson itself you can tie gene expression to brain region function (to talk about how function rises from brain structure properties). We’re also working on creating a new lesson that touches on exactly that!
Question: Are the morphology images from slices? If so, what’s the orientation of the image?
Luke: Yes, these images are from slices. The Technical white paper: Cell morphology and histology gives good details about orientation.
Question: Is this slide (re: large datasets) on your website? Very helpful to show students
Kaitlyn: The slide showing dissection and large datasets was made from figures found in the microarray survey white paper found in our documentation here: help.brain-map.org/display/humanbrain/Documentation.
Question: Do comparisons between gene expression taken from recently “living” brain samples (mice and human surgery) and long postmortem human brain help rule out biases in postmortem mRNA stability?
Kaitlyn: That’s a great question. The paper that Luke is talking about does this comparison. You can find it here (that particular analysis is described in the second paragraph of the results section): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6919571/
Question: Is this the paper Luke just referenced? https://www.biorxiv.org/content/10.1101/2020.02.03.932244v1
Kaitlyn: Yes!
Question: Is there any plan to tie the transciptome data to protein-level data and subcellular localization?
Luke: There are no immediate plans for a widespread proteomics study but there are smaller focused studies for specific genes of interest.
Question: Is the lab handout also available in .doc format, for editing? Thank you!
Kaitlyn: Yes, you can email communications@alleninstitute.org to request it.
Question: Referring to Allen Cell Types Database electrophysiology data: Is it mentioned what each stimulus is?
Luke: Yes; information about stimuli is available in the Documentation, Electrophysiology section (downloadable PDF here).
Follow-up Question: So a relevant question for students would be, which stim reaches threshold in a cell?
Luke: Yes, we agree. this is an important concept that this tool can help illustrate.
Question: it’s not statistically valid to calculate SDs on samples of n of 3, in most scientific experiments. As written, this could teach them some bad statistical habits. is there anything in the tutorial about selecting appropriate statistical methods?
Luke: Thank you. That’s a good point. The mitosis lesson plan gets into more details about statistics. https://alleninstitute.org/about/education-outreach/mitosis-and-microscopy/
Kaitlyn: Yes, that’s a good point. The idea behind having the students calculate the mean and standard deviation is to start getting them to practice that, but it’s a smaller sample size than they should use in real experimental life. As I mentioned, the lesson plan is meant to be customizable, so feel free to take that out.
Question: For inhibitory neurons, what is the “L” classification based on? e.g. L1 or L5. Does it refer to layers?
Kaitlyn: Yes. Layers.
Question: Are you including other animals’ brain atlas and RNA seq data in the website? Like rats or monkey?
Kaitlyn: A non-human primate atlas is available at brain-map.org, but it doesn’t have single cell RNA seq data in it. We don’t currently have rat data and we have no plans to add any.
Question: I know you had a webinar on the mitosis lab back in June but I missed that. Are you planning on dong that webinar again?
Kaitlyn: A recording of that webinar is available at https://alleninstitute.org/about/education-outreach/virtual-science-lab-webinars. We’re not planning to run it again live.
Question: Do you have any data for Hox genes?
Kaitlyn: Our human (and mouse) atlases have all genes in the genome, including Hox family genes. You can use the search box to search for them. Our transcriptomics explorer for the Allen Cell Types Database will also include those transcripts.
Question: To help instructors adopt these lesson plans, it would be helpful to provide more small sets of genes relevant for particular developmental or disease processes. Is there a place where instructors can share their own sets of genes used in their classes?
Kaitlyn: That’s a great question. You can either email us at communications@alleninstitute.org or post the gene list you used on the forum at community.brain-map.org as a response to this post. Also on the home page of the Allen Human Brain Atlas, we have pre-selected gene categories for various neurological conditions, and also general nervous system functions, that you can use to sort.
Question: How do students find out about internships?
Luke: Internships have some requirements, such as you must be a US Resident and over 18 years old. The applications open in December and are due in January for the following summer. Learn more about the internships at https://alleninstitute.org/careers/internships/.
Question: How many scientists are there at the Allen Institute?
Luke: Across all of the institutes, Brain Science, Cell Science and Immunology, we have about 150 post-PhD scientists, out of about 500 total employees. We have many other scientific staff positions, such as Research Associates, Engineers and Data Analysts. Learn more about our Brain Science team here.
Question: Are statistics specific to a single probe or an average of all the probes for an individual gene?
Kaitlyn: All statistics are calculated on a probe-by-probe basis.