mariesol04
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What are blood cells?

Postby mariesol04 » Sat Dec 05, 2020 11:43 pm

Hello, I am doing the science buddies project titled Taking Short Cuts related to transcription factors. I am planning on starting with blood cells and my target cells will be liver cells. I am having trouble reading the graphs on Amazonia. What type of cell is considered a blood cell? Should I change my starting cell?
Thank you for your help.

brandimiller610
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Re: What are blood cells?

Postby brandimiller610 » Sun Dec 06, 2020 6:35 pm

Hi mariesol04,

I hope you are having a great day. I have answered your questions about the "Taking Short Cuts" project on Science Buddies to the best of my ability.

The graph generated by Amazonia is a microarray; it tells you the expression for a particular gene in all cell/tissue types in the body. Based on the project procedure (https://www.sciencebuddies.org/science- ... to-another procedure), you will find the expression of all the transcription factors (TFs) listed in Table 1. Using the microarray, you assess the expression of the TF for your target tissue (which can be found by looking for your tissue name on the x-axis) and compare it to tissues that have similar expression on the microarray (this is what you record). According to the procedure, it seems that you choose one target tissue (so blood cells OR liver cells, not both). You could, of course, do the project for both and compare the expression of their major TFs. I do not believe you need to change your cell type; blood cells and liver cells are both indicated as potential types for this project and most of their TFs should be found on Amazonia.

I am not quite sure what you mean by "what type of cell is considered a blood cell?", but I think you are asking what type of cell is a blood cell. A blood cell is a hematopoietic stem cell (HSC), meaning it gives rise to blood cell components (such as red blood cells, white blood cells/innate immune cells, etc.) through hematopoiesis.

I hope I have helped answer your questions and understanding of the Amazonia microarray. If something remains unclear or you have additional questions, please feel free to add them on this forum. Good luck!

--Brandi

mariesol04
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Re: What are blood cells?

Postby mariesol04 » Mon Jan 18, 2021 5:34 pm

Hi thank you for the help.

I have another question related to this project. To make this project more challenging, I am determining which TF's will interact to form the target cell. How would I use the data that I collected from the KEGG database to support my answer?
Also, I mostly have data with observations (Amazonia, NCBI Gene Database). Is there any way to organize this data into a more statistical form?

Thank you so much!

Marie Kim

MadelineB
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Re: What are blood cells?

Postby MadelineB » Wed Jan 20, 2021 3:53 pm

Hello Marie Kim,

Since the Science Buddies guidelines for posting request that you not post duplicate posts, I've removed your most recent post. Thank you for patiently waiting for the expert who has been helping you. The experts are volunteers and may not be able to respond immediately.

Thank you and good luck with your project.
Madeline

mariesol04
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Re: What are blood cells?

Postby mariesol04 » Mon Jan 25, 2021 6:46 pm

Hi,

I was also wondering if you knew how this project would work in an real life experiment? I think that knowing how the transcription factors are taken and then used will help me analyze my data better.
Thank you again for your help!

Marie Kim

mariesol04
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Re: What are blood cells?

Postby mariesol04 » Mon Jan 25, 2021 6:47 pm

URGENT!!!!!
please look at above posts!!!!

koneill18
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Re: What are blood cells?

Postby koneill18 » Tue Jan 26, 2021 7:42 pm

Hello!

To find an answer to your question, you can start by using the Amazonia database to look for 3-4 transcription factors that, when taken together, are uniquely active in your target cell type. For example, let’s say you’re looking at 4 transcription factors that are expressed in the blood. Here are some made up examples of the tissues that each transcription factor is expressed in:

TF 1: Blood, kidney, pancreas
TF 2: Blood, ovary, small intestine, skin
TF 3: Blood, stomach, tongue
TF 4: Blood, spleen, liver, heart

All of these transcription factors are expressed in more than one tissue, but the blood is the only place where all 4 of the transcription factors are expressed, meaning that all 4 transcription factors used together could specifically make blood cells.

Once you have your transcription factors, you can search for them in the KEGG database and see if they’re involved in any of the same pathways. This can show you how the transcription factors are related and how they may work together to generate the target cell type.

You can also read through some scientific papers to see if any researchers have tried combining the specific transcription factors you picked to make your target cell. Here’s a link to the Science Buddies guide for finding scientific papers:
https://www.sciencebuddies.org/science- ... fic-papers

In real life, scientists would clone the genes corresponding to the transcription factors of interest into a circular piece of DNA called a plasmid. They add the plasmid to the stem cells in a cell culture dish and the cells take up the plasmids. The plasmids go to the nucleus of the cell where the transcription factors can bind to the cell’s DNA and tell it what genes to express. This was a simplified explanation of a pretty complex process, so let me know if you want a more in depth explanation!

In regards to your question about statistics, you’ll have to use more qualitative methods of analysis since your data won’t include any numbers for you to work with. You can organize your information into tables, like the one that’s shown in the Procedure section of the project. You can also make flow charts to show how the different transcription factors are related if you find out that they participate in the same pathways.

I hope this was helpful. If you have more questions or need clarification on anything, feel free to ask!

mariesol04
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Re: What are blood cells?

Postby mariesol04 » Tue Jan 26, 2021 8:20 pm

Thank you so much!!! I appreciate your help.

mariesol04
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Re: What are blood cells?

Postby mariesol04 » Fri Feb 05, 2021 5:33 pm

Hello,

I was wondering why it is necessary to calculate 90% of the average signal for this project? Thank you

koneill18
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Re: What are blood cells?

Postby koneill18 » Tue Feb 09, 2021 6:44 pm

Hi!

If the average signal coming from one of the other cell types is more than 90% of the signal from your cell type of interest, that means that it expresses the transcription factor at a very similar level to your cell of interest. Once you calculate the value for 90% of the average signal in your target cell type, you can compare that number to the average signals from the other cell types to help you identify which cell types express the transcription factor at the same level or at a higher level than your cell type of interest. That information helps you decide if that transcription factor is specific to your target cell type or not.

I hope that answers your question!


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