PMC

a Forest plot for the risk ratio (RR) of ORN development between pre-intensity-modulated radiotherapy (IMRT) extractions and post-IMRT extractions. b Forest plot for the odds ratio (OR) of ORN development between pre-IMRT extractions and post-IMRT extractions. c Forest plot for the RR of ORN development between pre-IMRT extractions and no pre-IMRT extractions. d Forest plot for the OR of ORN development between pre-IMRT extractions and no pre-IMRT extractions. CI confidence interval

Quality scores of the initial extractions, manual improvements and automatic improvements. a Box-plots of the quality scores for initial extractions, manually improved and automatically improved extractions with their medians as 88, 89 and 94. Green * shows their average quality scores which are 87 ± 6, 89 ± 6, and 93 ± 4. For outliers, green + represents a case that the LM does not exist which is a coronary artery anomaly; red * represents a case that the LAD is not automatically extracted; blue + represents a RD case that only the proximal part of the RCA was extracted; red diamond represents a case that the distal part of the LCX could not be extracted. b Bar-plots of the quality scores sorted by the scores of the initial extractions. Red, blue bars show the scores for the manually improved and initial extractions; green line shows the scores of automatically improved extractions. LM left main artery, LAD left anterior artery, LCX left circumflex, RD right dominant

Reproducible protein identification and quantitation from small amounts of tissue. (A,B) Venn diagrams illustrating overlap in unique protein groups (A), and unique peptides (B) identified by MaxQuant between 20, 5, and 1mg of tissue (n = 3 technical replicates for each group). (D Scatterplots of Log2 _LFQ protein intensities showing high reproducibility between replicates from 20 mg (D), 5 mg (E), and 1 mg (F) tissue extractions. Pearson correlation coefficients are shown in the top left corner of each panel. (G–I) Scatterplots of Log2 _LFQ protein intensities showing high reproducibility between averaged replicates from 1 mg extractions plotted against 5 mg extractions (G), 1 mg extractions plotted against 20 mg extractions (H), and 5 mg extractions plotted against 20 mg extractions (I) with Pearson correlation coefficients shown in the top left corner of each panel (n = 3 technical replicates for each group).

RNA integrity checking. Gel image generated by the automated electrophoresis system (Experion, Biorad). Lanes M – RNA molecular weight markers supplied with the Experion RNA StdSens analysis kit. Lanes PGTX beads – 1 μl of extracted RNA from distinct extractions using the PGTX solution combined with mechanical cell disruption with glass beads. Lanes Trizol beads – 1 μl of extracted RNA from distinct extractions using Trizol combined with mechanical cell disruption with glass beads. Lanes PGTX 95 – 1 μl of extracted RNA from distinct extractions using the PGTX solution combined with high temperature cell disruption. Lanes Trizol 95 – 1 μl of extracted RNA from distinct extractions using Trizol combined with high temperature cell disruption. Lanes Trizol std – 1 μl of extracted RNA from distinct extractions using Trizol according to general manufacturer's instructions. Lanes BPC – 1 μl of extracted RNA from distinct extractions using the BPC method. RNA integrity was kept for all extraction methods.