fionacho
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Inquiry: Direct Reprogramming of Cells

Postby fionacho » Tue Sep 29, 2020 10:00 am

Hello, I plan to do a project on the direct reprogramming of cells this year. I had a question on the procedure.

On the procedure, it says to look at every single graph on the Amazonia database under a certain transcription factor to record whether or not it is highly expressed in other cells that are NOT your target cell. By "every" graph, does it mean just every graph under "Human Body Index" or every graph under both "Human Body Index" AND "Embryonic and adult normal tissues"?

I was wondering about this because it seemed like the data from "Embryonic and adult normal tissues" varied a lot from the data under "Human Body Index".

Thank you!

koneill18
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Re: Inquiry: Direct Reprogramming of Cells

Postby koneill18 » Tue Sep 29, 2020 12:36 pm

Hello!

Cell reprogramming is a really interesting topic! Is this the project that you're doing? What is your tissue type of interest?
https://www.sciencebuddies.org/science- ... er#summary

The procedure calls for you to look at every graph on the page, including all the graphs from both Human Body Index AND Embryonic and adult normal tissues. It's totally normal for different microarrays to give variable data. This can be due to slight differences in the samples the researchers used and the experimental conditions. Looking at as much data as possible helps you find overall trends and patterns. You can record how many out of the total number of graphs show high expression of the transcription factor in other cell types besides your cell type of interest. If many of the graphs show high expression of the transcription factor in other cell types, that means the transcription factor isn't specific to your cell type of interest and it could generate different cell types that you don't want.

I hope this helps. Let me know if you have other questions!
koneill18

fionacho
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Re: Inquiry: Direct Reprogramming of Cells

Postby fionacho » Tue Sep 29, 2020 3:27 pm

Thank you so much!

My partner and I haven't decided the target cell yet - probably one of the top 3 most needed transplants (kidney, liver, heart). I'll make sure to analyze all of the graphs!

koneill18
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Re: Inquiry: Direct Reprogramming of Cells

Postby koneill18 » Tue Sep 29, 2020 5:03 pm

Sounds great! Let me know if you have any other questions.

fionacho
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Re: Inquiry: Direct Reprogramming of Cells

Postby fionacho » Tue Jan 05, 2021 12:09 am

Good evening!

I had another question about this project. My partner and I ended up choosing the direct reprogramming of the heart cell. We have been analyzing the transcription factors for quite a while now, and have found no graphs whatsoever that are close to being a good match. In fact, all of them have a lot more than 5 other cell types that express the transcription factor at higher rates than the heart cell. Feeling a bit confused, I decided to skim through the graphs we have not yet analyzed to take a look at them, but again, they all look unpromising. Currently, it looks as if none of the graph show that any of the transcription factors are remotely good matches for the heart cell. Is this supposed to be happening, or are we doing something wrong?

Thank you once again!

koneill18
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Re: Inquiry: Direct Reprogramming of Cells

Postby koneill18 » Tue Jan 05, 2021 8:26 pm

Hello!

I looked through a few of the transcription factors listed for the heart, and you're correct that they're also expressed by a lot of other tissue types. For this reason, it's pretty common for scientists to use multiple transcription factors together to try to reprogram cells. One transcription factor alone might not be enough to get the job done. For your project, one option would be to look at all of the graphs for each transcription factor in the list and pick the one that has the highest level of transcription in the heart- even if it's also expressed by other tissue types. Your other option is to do your own research to look for other transcription factors that aren't in the list.

I did a web search for "transcription factors for programming cardiac cells." Here's a link to an article that I found:
https://www.embopress.org/doi/full/10.15252/embj.201490563
In the second paragraph of the introduction, it says that 3 cardiac transcription factors that can be used to program heart cells are Gata4, Mef2c, and Tbx5.

I looked up Tbx5 in Amazonia, and it looks like it's expressed at pretty high levels in the heart in comparison to other tissues.
http://amazonia.transcriptome.eu/expression.php?geneId=Hs.381715
One of the 3 transcription factors I just mentioned, or one of the other ones mentioned in that article, might give you better results than the transcription factors listed in the project guide.

I hope this helps!

fionacho
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Re: Inquiry: Direct Reprogramming of Cells

Postby fionacho » Mon Jan 18, 2021 6:44 pm

Thank you so much! I think we will look for viable transcription factors using past research articles.


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