Table S2
Description
Supplementary Table S2. Results of SQuIRE differential expression analysis on TEs. Quantification of the locus specific expression of TEs in SK-UT-1 cells treated for 6 or 24 hours with different HDAC inhibitors (NKL54, TMP195 and SAHA).
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Locus-specific TEs expression was quantified using SQuIRE with default parameters. Raw counts were normalized using the DESeq2 default median of ratios approach (using the counts function with the normalized = TRUE parameter) to account for both TEs dispersion and different sequencing depth across samples. For further information see the Materials and Methods of the related manuscript
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Funding
Associazione Italiana per la Ricerca sul Cancro
IG 2021 - ID. 26200 project – P.I. Brancolini
Interreg Italia-Osterreich
ITAT11-018 SENECA