Transposon DNA sequences facilitate the tissue-specific horizontal transfer: te expression supplementary datasets

These datasets contain data on analyses of TE expression stability. Raw RNA seq counts were processed using DESeq2 R package. Low count genes and TEs were removed. Counts across samples were normalized for library sizes and log-transformed using 'regularized log' transformation. Batch normalization was performed on log-transformed data with ComBat function from sva R package.  Expression variability (EV) of TEs and genes (probes) was estimated using the previously described method [1, 2].

1. Bashkeel, N., Perkins, T.J., Kærn, M. et al. Human gene expression variability and its dependence on methylation and aging. BMC Genomics 20, 941 (2019). https://doi.org/10.1186/s12864-019-6308-7
2. Alemu EY, Carl JW Jr, Corrada Bravo H, Hannenhalli S. Determinants of expression variability. Nucleic Acids Res. 2014;42(6):3503-3514. doi:10.1093/nar/gkt1364

PC.zip - the results of TE expression and stability in prostate cancer.

• 0.PC.RlogMAD.pdf - count barplots for TE identified with MAD criteria
• 0.PC.RlogSD.pdf - count barplots for TE identified with SD criteria
• 0.PC.TE.rlogcpm.mad.xls -stability measures according MAD (median absolute deviance) criteria 
• 0.PC.TE.rlogcpm.sd.xls - stability measures according SD criteria 
• 0.PC_TE_bootstrap.pdf - TE expression stability
• PC.deseq.logCPM.csv - TE log transformed expression matrix 
• PC.TE_count_table.csv - TE raw count matrix 
• PC_Deseq2data.Rdata - R data object with deseq objet, raw and normalized counts

MM.zip - the results of TE expression and stability in multiple myeloma.

• 0.MM.RlogMAD.pdf - count barplots for TE identified with MAD criteria
• 0.MM.RlogSD.pdf - count barplots for TE identified with SD criteria
• 0.MM_TE_bootstrap.pdf - TE expression stability
• MM.deseq.logCPM.csv - TE raw count matrix 
• MM.rlog.mad.xlsx- stability measures according MAD (median absolute deviance) criteria
• MM.rlog.sd.xlsx - stability measures according MAD (median absolute deviance) criteria 
• MM.TE_count_table.csv - TE raw count matrix 
• Myeloma_Deseq2data.Rdata - R data object with deseq objet, raw and normalized counts