Hello everyone, I am working with GTEx v10 RNA-seq TPM data (currently liver) and have a few questions regarding sample IDs, donor matching, and version updates. I would really appreciate clarification, as I am relatively new to working with GTEx data.

1. Tissue site ID inconsistency within the same organ: In the GTEx v10 TPM files (e.g., liver), sample IDs look like the following: GTEX-111FC-1226-SM-HAV27 , GTEX-11DXY-0526-SM-5EGGQ , GTEX-11DXZ-0126-SM-5EGGY etc. According to the GTEx FAQ: “The format of the sample ID is GTEX-[donor ID]-[tissue site ID]-SM-[aliquot ID]. The donor ID should be used to link between samples. The tissue site ID mostly refers to the tissue site, but we do not recommend using it for tissue site designation.” Since I am extracting RNA-seq data from only one organ (liver), I was expecting the tissue site ID (e.g., 1226, 0526, 0126) to be consistent across samples. Why do these tissue site numbers differ for samples from the same tissue? Does this reflect different anatomical sub-sites, collection batches, or something else?

2. Linking RNA-seq data to histology data using donor IDs: I understand that the core identifier is the donor ID (e.g., GTEX-111FC), and I am using this ID to link RNA-seq data and donor histology information for a specific organ (I hope this is correct?). However, when I download and open the consolidated histopathology file from the Histology Viewer, I notice that many subjects who have histology records for a given organ do not have corresponding RNA-Seq data. Is this expected behavior? Are RNA-Seq data only available for a subset of samples or tissues, or am I missing a specific filtering or mapping step?

3. New tissue sites in GTEx v11 despite “no new samples or donors”: GTEx website states that: “GTEx v11 updates the GTEx v10 data to use GENCODE v47 annotation. It contains no new samples or donors compared to v10.” While I understand that the donors are the same, I noticed that new tissue sites (e.g., small_intestine_terminal_ileum) appear in v11. Does this mean:

• these tissue samples already existed in v10 but were reclassified in v11, or
• that additional anatomical regions were sampled retrospectively from preserved specimens of the same donors?

I would appreciate clarification on how new tissue labels can appear without introducing new samples.

Thank you very much for your time and patience. Any guidance or pointers would be extremely helpful.

Please Note: I only have access to open access GTEx data.