Hi, I am wondering if resilient samples in syn24175554 have FPKM values or just FASTQ files. I can see that some of the resilient samples are in the harmonised ROSMAP metadata files, but I cannot find their IDs in the FPKM files. Any help would be much appreciated! Best wishes, Olivia.

Created by Olivia Todd Liv_T97
Hi @Liv_T97, We are planning to release the new study in the next few weeks, ideally by the end of November. I'll keep you posted if any major delays come up, but we are in the final stretch. Thanks for your patience! Will
Hi @wpoehlm, Thank you for your response! That is great news, and should really help with my analysis. Any idea when we can expect the new harmonisation study to be uploaded? All the best, Olivia.
Hello @Liv_T97, I just spoke with our analyst about the resilient samples. We weren't able to run differential expression analysis on these samples due to low numbers, but we will publish normalized CQN counts for them regardless. There will also be unprocessed counts in TPM and raw count formats. The analysis methods for the updated harmonization study should also be more clearly documented. Hope this helps! Best, Will
Hi Will, Can you just confirm that the resilient samples will be included (and processed to CQN) in the new harmonised study? All the best, Olivia.
Hi Will, Thank you for your response! I have looked through the samples in https://www.synapse.org/Synapse:syn25817661, and I am wondering how these counts were generated? Specifically, did the samples in the subfolder 'Gene Expression (Raw Gene Counts)' in the RNASeq Harmonisation Study undergo similar reference genome alignment to those in the normalised count folder (Gene Expression (Normalised Counts and Differential Expression). I can't figure out how these samples have been processed relative to one another... I hope this makes sense :) I will keep an eye out for the updated harmonisation study! All the best, Olivia.
Hello @Liv_T97, Raw gene counts (un-normalized) for these samples can be found in the [RNASeq Harmonization Study](https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage/StudyDetails?Study=syn21241740). Specifically, the counts for Rosmap cognitive resilience can be found in https://www.synapse.org/Synapse:syn25817661. Please note that we will soon be releasing an updated harmonization study that processed the same data through a newer reference genome and pipeline. This release will include raw counts, TPM, and CQN normalized matrices. We will recommend using these updated counts as soon as they are available (we are aiming for the data release at the end of this month, but if not it will be In October). Best, Will

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