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Data resource IBDMDB
#1

I’m very interested in your research work, and prepare to perform personalized analysis for IBD individuals based on your database.

    I downloaded all the available data through the provided weblink. According to the file "hmp2_metadata.csv",column "data_type",the individualized omics data needs some supplement:
    1. host_genome: genetic data of each sample were not provided.
    1. Metatranscript: the gene family, pathway and enzyme commission information were provided ,but not all the gene expression data of each sample.
    1. Proteomics: the differentially expressed proteins between CD/UC non-IBD were provided, as well as enzyme commission information and protein pathway information. But we did not found information about all protein expression data of each sample.
    1. Methylome: there is no link to download the methylation data of each sample.
  • 5.Serology:cs there is no raw data for expression of serological markers.

    1. Stool_16S: no link for Stool_16S were provided.

      I wonder if we can get the right to use these missing omics data? I promise to use it only for scientific purposes. Thanks.

#2

Hi User,

Below, I have listed the sources:

  1. host_genome: The host genome data is available in dbGAP. Please direct to this link - Study Accession : phs001626.v1.p1 for more information.

  2. Metatranscript: The raw metatranscriptome files are available for download here.

  3. Proteomics: The protein expression data of each sample are in their own files.

  4. Methylome: The Methylome data is available in dbGAP as well.

5.Serology: The raw serology is included in the metadata file.

  1. Stool_16S: Not Available
#3

Dear Professor Dr.Maharjan:

Thanks for quick reply.

I went to the dbGAP database to search for them, and came to the conclusion that I need to apply through https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?login=&page=login.

In fact, for these omics (host genome, Methylome, Metatranscript, Proteomics, Serology), we just need a merged file containing annotation/expression data of each sample, similar to “iHMP_metabolomics.csv”. we do not need to download the original raw data. Is it convenient for you to provide these data ?

For serology, I only found two serological indicators of “CRP (mg/L)” and “ESR (mm/hr)” in “hmp2_metadata.csv”. I wonder if there is any omission?

Best Regards.