Hello! I aim to acquire blood transcriptomics data from the Parkinson’s Disease Biomarkers Program (PDBP) website. I possess a valid access login account, but I cannot locate where to access this specific data.
For example, when I search for study forms and data that are related to “Genomics”, I find these:
When I look up for the “Other Omics” I find these:
However, when I download the different forms that are present in those both sections (example: PDBP Next Generation Sequencing Dataset, PDBP SNP Array Data Set, PDBP Bioessay Form and PD SomaLogic Platform), none of them have transcriptomics information, just genomics, as per the evaluation of a bioinformatician I work with. From what I know, the forms that contains “PDBP” in their names are those that adhered to a common protocol that a lot of the substudies participated, and where this information can be found. I also explored the forms that does not have PDBP in their name, but didn’t find it also.
I know that the AMP-PD platform possesses information on PDBP transcriptomics (PDBP | AMP-PD), however I wanted to obtain those data from the original dataset also, however, if it is better to download it from AMP-PD, I’m open to learning how to do it and obtain my transcriptomics data from there.
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I’ve accessed the PDBP transcriptomics data through AMP PD but not directly from PDBP. This might be an easier route. You can always subset to PDBP and either use the clinical data from PDBP or the harmonized data from AMP PD.
What data type are you looking to get? The raw fastq files? Or something like count data? @vdardov has a nice post about accessing AMP PD data and an introduction to the Terra platform. If you are looking for a smaller file like count data, you can also download it (smaller egress fees that way) and work with it from there.
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Thanks for the answer. I’m applying for AMP-PD access and will try to get data from there! Seems easier
EDIT: I’ve sent an email to the PDBP team, and they replied the following:
"There is limited transcriptomics data in PDBP that was provided by Dr. Judith Potashkin (“Blood RNA biomarkers of Parkinson’s disease and Progressive Supranuclear Palsy (U01)”), and by Dr. Jing Zhang (“Large Scale Biomarker Discovery and Validation for Parkinson’s Disease (U01)”). You can go into the PDBP Query tool, pull up these two studies, and access their transcriptomics data that way.
However, these are relatively smaller samples. A much larger transcriptomics effort was undertaken with PDBP subjects through the Accelerating Medicines Partnership Parkinson’s Disease (AMP PD), and that data can be accessed through the AMP PD portal. Along with PPMI transcriptomics data (both patient cohorts were analyzed using the same transcriptomics protocol). The AMP PD data for the PDBP cohort can only be accessed through the AMP PD portal—it is not available through the PDBP DMR. If you want larger sample sizes, I would suggest accessing the transcriptomics data through AMP PD."
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