We ran #deconvolution on the 110 bulk RNA-seq samples, with six selected methods: #DWLS, #bisqueRNA, #MuSiC, #BayesPrism, #hspe, and #CIBERSORTx. The methods returned a wide range of proportion estimates 📊

Using #RNAseq in combination with #CIBERSORTx on paired tumor scrapes, 3D organoids and 2D cultured cells, we discovered that zero-passage organoids generally retain the proportion of luminal cells, whereas 2D cultures did not, illustrating the importance of #matrigel cues.