Transcriptome analysis and ribosome footprints in engineered chromosome 3 and chromosome 8 isogenic aneuploidy cell model.

We analyzed two isogenic aneuploidy models. The first model is the chromosome 3 isogenic aneuploidy model, which includes three cell types: chromosome 3 WT, 3q gain, and 3p loss. By comparing with chromosome3 WT, we evaluated the overall transcript expression changes in 3q gain and 3p loss cells. Additionally, by comparing with chromosome3 WT, we assessed the changes in ribosome-protected fragments in 3p loss cells. The second model is the chromosome 8 isogenic aneuploidy model, which includes two cell types: chromosome 8 WT and 8p loss. By comparing with chromosome 8 WT, we evaluated the overall transcript expression changes in 8p loss cells. Overall design: mRNA expression was quantified in chromosome 3 WT, 3q gain, and 3p loss cells, with three biological replicates for each genotype. Additionally, ribosome-protected fragments were quantified in chromosome 3 WT and 3p loss cells, also with three biological replicates. Furthermore, mRNA expression was measured in chromosome 8 WT and 8p loss cells with three biological replicates.