Hello,
I am currently utilizing the HBTRC SNP data for eQTL discovery. I have gone through imputation and have ped and map files ready as input for matrixEQTL. The only issue I have right now is that the sample names between the SNP data on synapse and the expression data on GEO are completely different. The sample names for the HBTRC dataset are formated so: 15778:15778, while the GEO expression data sample names are like this: GSM012897. Does anyone know if there is a file that matches the different sample names? I understand that this dataset was updated in 2015 which may have been the time when the sample names were switched.
Created by Harrshavasan Congivaram HarrshaCongivaram Most of the data in the AD Portal comes from grants supported through a variety of NIA funded programs with a mandate to share. HBTRC was a pre-award dataset (ie, no sharing obligations) with SNP genotypes and gene expression from the PFC. We were not involved in the deposit of the larger gene expression dataset to GEO, and unfortunately do not have have a mapping key between the two Hello @Mette,
Our lab has previously attempted to contact the author of the original study (Dr. Bin Zhang) and the person who uploaded the data GEO (Dr. Jun Zhu). We have not heard back from either contact so we are unable to proceed. Is there another way by which we could contact these individuals? The deposit to GEO was done independently of the data hosted in the AD Knowledge Portal. I recommend reaching out to the contact author for the citation of the GO data The relevant synapse ID is syn20808201 and the relevant GEO dataset is GSE44772
Drop files to upload
Discrepancy between sample naming of HBTRC SNP data and corresponding expression data available on GEO page is loading…