IBDMDB sample details

Data resource IBDMDB
1

Hi Sagun and Curtis - How many samples from the IBDMDB have 16S data available? I downloaded the sample details available on the iHMP site and filtered on ‘biopsy_16S’ and ‘stool_16S’ which returns 358 samples. However, the same dataset (I think) on QIITA (ID# 11484) indicates that there are sample details for 2951 samples.

2

Hi dpbisme,

If you are pulling the samples from QIITA, I’d be careful to see if you aren’t lumping in the HMP1 data as well; that had a lot more 16S data generated.

Thanks,
Sagun

3

Hi Sagun - Can you take a look at the QIITA page here: https://qiita.ucsd.edu/study/description/11484

My take is that is this only 16S data, and only from HMP2. The sample numbers just don’t square with what I have metadata for from the IBDMDB site. Can you confirm how many samples have 16S data? Also, you mentioned in an earlier communication that there may be some clinical metadata deposited to NCBI’s dbGAP. Is that still the case? If so, do you have an accession number for these?

Thanks.

Dan