How to get metagenomic healthy reference?
0
0
Entering edit mode
4.9 years ago
agata88 ▴ 820

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

metagenomic 16S HMP • 1.1k views
ADD COMMENT
0
Entering edit mode

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/

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 ...

ADD REPLY

Login before adding your answer.

Traffic: 1031 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6