There are 38 samples in the normalized counts table at first (syn64333318). I removed samples with IDs 0128, 0129, 0130 (2 each, a tumor and an organoid) as per Dr. Soragni's 2/3/25 email due to quality issues.

That leaves 32 samples in the transcriptomic data. The data in syn61894657 confirm this - 64 rows, one for each paired read, 64/2 = 32 total samples to include with RNAseq data.

There are 15 samples in the genetic SNV mutation data (syn61894695), 2 of which do not overlap with transcriptomic data, for a total of 34 samples.

The sample sheet also contains information for one id (SARC0139) that is not present in either transcriptomic or mutation datda, but from with other samples (139_1 and 139_2) are derived from and have the same sample info.

32 transcriptomic IDs + 2 additional genetic mutation IDs + 2 samples for 139 IDs (tumor and organoid) = 36 total IDs in the sample sheet.

The paper mentions that 'select samples' were sent for genetic mutation analysis. All sample IDs in Al Shihabi et. al. Figure 2B (vertical at the top of the figure) that display transcriptomic data were present for both Tumor and Organoid in syn64333318.

sarcpdo missing many organoids #367

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