Fig. 2. High temperatures improve yield of small mouse fragments with FFPE-CUTAC.

a Scheme, where TL Prot K is Thermolabile Proteinase K (New England Biolabs). Created with BioRender.com. b Arrhenius plot showing the recovery of fragments mapping to the Mm10 build of the mouse genome as a function of temperature. Deparaffinized FFPEs were scraped into cross-link reversal buffer (20) containing 0.05% Triton-X100, needle-extracted, and divided into PCR tubes for incubation in a thermocycler at the indicated temperatures. c Same as (b) except for fragments mapping to the Rhodococcus erythropolis genome. d Scatter plots and R² correlations between total fragments recovered versus R. erythropolis and the summed totals for 6 other bacterial species discovered in BLASTN searches of unmapped reads (Escherichia coli, Leifsonia species, Deinococcus aestuarii, Mycobacterium syngnathidarum, Vibrio vulnificus, and Bacillus pumilus). e Comparison of average overall length distributions between tumor and normal brain, combining samples from all 3 brain tumors (YAP1, PDGFB and RELA). RNAPII-Ser5p: 15 samples; RNAPII-Ser2,5p: 15 samples; H3K27ac: 15 samples; 50:50 mixture of RNAPII-Ser5 and RNAPII-Ser2,5p: 14 samples. For each sample, mouse fragment lengths were divided by the total number of fragments before averaging. Lengths are plotted at single base-pair resolution. f Average length distributions for on-slide samples grouped by cancer driver transgene (YAP1: 12 samples; PDGFB: 7 samples; RELA: 12 samples) and Normal brain: 10 samples. Data are presented as mean values +/- SD in (e, f). Source data are provided as a Source Data file.