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100K GFP-positive

A. B. Mir93-Sensor-GFP. C. D. 100K GFP-negative. 100K GFP-positive. 10K GFP-negative. 10K GFP-positive. 1K GFP-negative. 1K GFP-positive. 1K Unseparated. 100K Unseparated. Tumor generated from GFP-positive cells. Tumor generated from GFP-negative cells. DAPI. DAPI. DAPI.

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100K GFP-positive

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  1. A B Mir93-Sensor-GFP C D 100K GFP-negative 100K GFP-positive 10K GFP-negative 10K GFP-positive 1K GFP-negative 1K GFP-positive 1K Unseparated 100K Unseparated Tumor generated from GFP-positive cells Tumor generated from GFP-negative cells DAPI DAPI DAPI GFP GFP+ GFP- GFP GFP Figure 1 (SUM159)

  2. B A Lung Spine Brain DAPI Annexin V-APC CONTROL DOX 0.13% 4.47% 0.14% 2.09% 0.53% 8.86% 6.78% 51.9% 56.4% 39% 24.2% 66.4% 12.5% 18.9% 52.1% 45.7% DOCETAXEL E C D DOX + DOCETAXEL F H Treatment Start Treatment Stop Treatment Start Treatment Start G Treatment Stop Treatment Start Treatment Start Figure S1 (HCC1954 In vitro, in vivo)

  3. Lung Leg DAPI Annexin V-APC Treatment start Heart Kidney B A CONTROL Pan-ck Pan-ck Pan-ck Pan-ck Treatment stop Treatment start Treatment start DOX Pan-ck Pan-ck Pan-ck Pan-ck DOCETAXEL Pan-ck Pan-ck Pan-ck Pan-ck E D C DOX + DOCETAXEL 0.09% 1.12% 0.06% 1.61% 0.4% 42.8% 0.65% 44.65% Pan-ck Pan-ck Pan-ck Pan-ck 92% 6.83% 90.8% 7.5% 27.4% 29.4% 30.1% 24.6% Treatment Start F H Treatment start Treatment stop G Figure 2 (SUM159)

  4. A B Treatment Start Treatment Start Figure S2 (MC1, UM2)

  5. A B D SUM159-Neg-DsRed SUM159 Non-infection SUM159-mirZip93-DsRed C SUM159-mir93 control SUM159-mir93 DOX Figure S3 (SUM159)

  6. A D B E C Treatment start Figure 3 (MCF7)

  7. Non-CD24-CD44+ CD24-CD44+ ALDH- ALDH+ ALDH- ALDH+ Figure S4

  8. TET-inducible mir93 lentivirus infected SUM159 (SUM159-mir93) A FACS ALDH- cells ALDH+ cells in suspension culture +/- Tetracycline (10 hrs) CTRL DOX CTRL DOX RNA isolation Affymetrix array CTRL DOX CTRL DOX RMA method 352 probesets downregulated with at least 2-fold changes 2110 probesets downregulated with at least 2-fold changes Compare to the predicted targets from TargetScan 12 Overlapped targets (0 stem cell genes) 127 Overlapped targets (>24 stem cell genes) B Figure 4 (SUM159)

  9. Table S1

  10. Figure S5 (HCC1954)

  11. B A CTRL 0.86% G0/G1: 64% S/G2/M: 34% DOX 47.31% 57.47% 48.58% 39.08% G0/G1: 42% S/G2/M: 53% SUM159-mir93 Figure 5

  12. CTRL DOX G0/G1: 31% S/G2/M: 68% G0/G1: 47% S/G2/M: 48% HCC1954-mir93 G0/G1: 53% S/G2/M: 42% G0/G1: 47% S/G2/M: 49% MCF7-mir93 Figure S6

  13. Ki67 MCM7 DAPI Merge TOTAL ALDH+ ALDH- Figure S7

  14. stem cell Mir93 - Mcm7 - Proliferating early progenitors Myc Self-renewal Differentiated cells Mir93 + Mcm7 + Quiescent stem cell pool SUM159 Mir93 - Mcm7 - ALDH+ Mcm7 Mir93 Mcm7 HCC1954 mir93 E2F1 Differentiation Cell proliferation CSC MCF7 ALDH- Figure 6

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