Fig. 1

Repeat element expression in AML patient samples (Uniklinik Freiburg). a Fraction of repeat transcripts that align to the main repeat classes in the CD34 + control and in the M1, M2 and M4 AML patient samples (Uniklinik Freiburg). 40% of reads consist of SINE/ALU repeats, around 30% are LINE elements, 9% LTR/ERV, and between 0.1 and 0.3% are Satellite repeats. Samples are grouped into CD34 + control and the M1, M2 and M4 AML subtypes. Error bars represent the standard error of the mean (SEM). b MA-plots (mean expression versus the log2 fold change) depicting changes in repeat expression in the in the CD34 + controls (n = 5) and the three AML subtypes: M1 (n = 2), M2 (n = 3) and M4 (n = 3). X-axis indicates the baseMean values and y-axis the log2 fold change values. c/d Inter-patient variation plots show normalized read counts for distinct repeat types in Satellite repeats (c) or LTR/ERV elements (d). Each data point represents one sample for each of the CD34 + control (n = 5) and AML samples (n = 8). e/f Coverage plots represent transcript reads that are aligned to consensus repeat sequence for distinct repeat types in Satellite repeats (e) or LTR/ERV elements (f). Per-base coverage is normalized to average 1X coverage as determined using bamCoverage from DeepTools