Hello Team,
I have created full metadata for ROSMAP by combining clinical and bio specimen metadata files.
I was referring published Nature paper which uses ROS single nucleus data.
Their metadata file https://www.nature.com/articles/s41586-019-1195-2#MOESM1 includes gpath , amyloid and plaq_n variables .
I could not see them in clinical csv or codebook.
Is there any other metadata file where those variables included?
thanks,
Shreya
Created by Shreya Paithankar shreya1704 Hi @shreya1704,
The full gene expression [matrix](syn3505720) has the same number of patients as the two batch-normalized plates you referred to and should be all the same patients. Can you identify which patients are missing (and also please include synapse IDs when referencing files)?
I am not sure what you are working on, but I will also refer you to the more recent RNAseq harmonization efforts, which have more samples and better provenance for tracking how the pipelines were constructed, where the files came from, and methods for differential expression analysis. Updated ROSMAP expression matrices, as well as rnaseq data from the MSBB and Mayo cohorts, are all here: [RNAseq Harmonization Project](syn21241740)
Best,
Laura
Thanks for sharing the information Laura.
I also have question about bulk rnaseq data.
There are two separate normalized files : ROSMAP_RNAseq_FPKM_gene_plates_1_to_6_normalized.tsv and ROSMAP_RNAseq_FPKM_gene_plates_7 to_8_normalized.tsv.
1. The other FPKM file is not the combination of these 2 files?
2. I could not find few patients in those FPKM files.
Hi @shreya1704,
Unfortunately those additional measures of neuropathology found in the 2019 Mathys et al. data set were not included in the clinical and demographic data that Rush agreed to post in the AD Knowledge Portal for all ROSMAP participants. In order to access this data, you will have to apply directly to the Rush Alzheimer's Disease Center (RADC) [Resource Sharing Hub](https://www.radc.rush.edu/requests.htm). The variables you are looking for in found in the '[Pathology](https://www.radc.rush.edu/docs/var/overview.htm?category=Pathology)' category, and you will need to follow the RADC directions requesting access to this data through the Limited Data Sets request process.
Best,
Laura
Drop files to upload
ROSMAP clinicopathological parameters page is loading…