Hello,
I am working on a Science Buddies project that requires the use of the Amazonia microarray database, but the site is unfortunately down on my end. I saw an earlier post from a few years back mentioning that the site wasn't working for them either and a working solution was not mentioned. It seems that the site still hasn't been fixed, and I'm not exactly sure if there is another microarray tool that can help complete this project. Help is appreciated... Thanks!
Here is the link to the project: https://www.sciencebuddies.org/science- ... background
Amazonia Microarray Database
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Re: Amazonia Microarray Database
Hi RasikaS - I am sorry that this resource for the project isn't available. I believe the site is no longer available, and the project needs to be updated to reflect that.
If you are able to change your project, you might want to consider doing that.
You can browse other related projects in:
Genetic Engineering: https://www.sciencebuddies.org/science- ... ngineering
Medical Biotechnology: https://www.sciencebuddies.org/science- ... technology
If you want to continue with this project, you can try this database instead: https://gtexportal.org/home/
The directions for the project will not be a perfect match since the project wasn't written for this resource, and we have not tested the project with this resource.
This video gives an overview of what GTEX is: https://youtu.be/PhK186A7Ryo
This video is a specific tutorial of how to find information about a gene in GTEX: https://youtu.be/39eT804VljI
Amy
Science Buddies
If you are able to change your project, you might want to consider doing that.
You can browse other related projects in:
Genetic Engineering: https://www.sciencebuddies.org/science- ... ngineering
Medical Biotechnology: https://www.sciencebuddies.org/science- ... technology
If you want to continue with this project, you can try this database instead: https://gtexportal.org/home/
The directions for the project will not be a perfect match since the project wasn't written for this resource, and we have not tested the project with this resource.
This video gives an overview of what GTEX is: https://youtu.be/PhK186A7Ryo
This video is a specific tutorial of how to find information about a gene in GTEX: https://youtu.be/39eT804VljI
Amy
Science Buddies
Re: Amazonia Microarray Database
Hello,
Thank you so much for providing an alternate resource! I am in the middle of this project, and I am unable to find the average signal of cell types (For example, the directions state that the average kidney signal is 166.7). It would be great if you could let me know where to find this on GTex.
Thank you so much for providing an alternate resource! I am in the middle of this project, and I am unable to find the average signal of cell types (For example, the directions state that the average kidney signal is 166.7). It would be great if you could let me know where to find this on GTex.
Re: Amazonia Microarray Database
Hello!
When you open the GTEx Portal homepage, type the name of the gene in the box that says "Search Gene" in the upper righthand corner. Once you do that, it should take you to a page called "Gene Page." If you scroll down, you'll see a section called "Bulk Tissue Gene Expression" that shows you the level of gene expression in all different tissue types. The numbers will be different from what you'd see in Amazonia because they're expressed in different units. Gene expression in GTEx is expressed as TPM, which stands for transcripts per million. This means that for every 1,000,000 RNA molecules in the sample, x came from your gene of interest. Even though the numbers are different from Amazonia, you should still be able to compare gene expression between the different tissues.
I hope this helps!
When you open the GTEx Portal homepage, type the name of the gene in the box that says "Search Gene" in the upper righthand corner. Once you do that, it should take you to a page called "Gene Page." If you scroll down, you'll see a section called "Bulk Tissue Gene Expression" that shows you the level of gene expression in all different tissue types. The numbers will be different from what you'd see in Amazonia because they're expressed in different units. Gene expression in GTEx is expressed as TPM, which stands for transcripts per million. This means that for every 1,000,000 RNA molecules in the sample, x came from your gene of interest. Even though the numbers are different from Amazonia, you should still be able to compare gene expression between the different tissues.
I hope this helps!