Entering edit mode
7.4 years ago
agata88
▴
870
Hi all!
I would like to ask you about the Human Microbiome Project database. I need fastq SRA samples for 16S metagenomic analysis that will include healthy stool results in 3 groups of age:
infants
adults
old people
Do you know if such data is publicly available? And if it is could somebody tell me were I should look for it?
I would really appreciate for help,
PS. Maybe you know other database including such information?
Agata
Dear Agata, look at the upper site.
http://ihmpdcc.org/HMQCP/healthy/index.php
and a paper below:
Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3374619/
This database contains 198 samples you are looking for, almost at the bottom of the page:
http://www.hmpdacc.org/HMASM/
Thank you natasha,
Do you know where I can find information about the age of SRR samples? I need to group 20 fastq SRR samples to group of 0-2 age, 3-18 etc.
I understand it, but I think it may be the hardest part.
If you simply ask in google "the age of SRR samples"
you get this:
http://www.epidemiolog.net/evolving/Standardization.pdf the age is inside
But there are many other parameters, I have some doubts if these data are available.
The main problem - you need healthy people.
In case of any disease these age groups are usually available.
http://jvi.asm.org/content/89/4/2425.full
I know that the data about age is not publicly available in HMP database, unfortunately. To get this information I need an extra access authorized by a group of people. I am not sure I am going to get this since I am no longer a student ... too bad ...