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Kourtidis Et Al Table S1. ShRNA sequences used in the present study* shRNA mature sequence ERBB2 CCCTGGCCGTGCTAGACAA NR1D1 GGCATGGTGTTACTGTGTA PBP CCGAGTTCCTCTTATCCTA MAP2K6 CAGATGACCTGGAGCCTAT SPINT1 CTGTGTAGTTTGTGCTGTA PFN2 AGCATTACGCCAATAGAAA MKI67 GCTACAAACTCCTAAGGAA TPD52 CTGTGAGATTCCTACCTTT BNIP3L AGCAGCAATGGCAATGATA LASP1 GGACCAGATCAGTAATATA CA9 CTTTGAATGGGCGAGTGAT FADS2 CCCATAGGGAGCTGATCGT ERBB3 CTACCAGTTGGAACACTTA GRB7 CTCGCCATCTGCATCCATC STARD3 AGGAGATCATCCAGTACAA FASN CTGGCCCAGGCTGAAGTTT ACLY GGGAGGAAGCTGATGAATA ACACA CACATGACCTTAAGATTAT MDH1 CGAGCTAAAGCTAAATTG ME1 GGCTTTATCCTCCTTTGAA *all shRNA sequences used in the present study can be retrieved in http://codex.cshl.edu Table S2. Primer pairs used for qRT-PCR in the present study gene forward primer reverse primer ERBB2 5’-AGACACGTTTGAGTCCATGCC-3’ 5’-ATCCCACGTCCGTAGAAAGGT-3’ NR1D1 5’-CCGTGACCTTTCTCAGCATGA-3’ 5’-CACTGTCTGGTCCTTCACGTTG-3’ PBP 5’-GGCAACAACCCAATGAGTGGT-3’ 5’-ATGCCGATCTTTGATGCTCATG-3’ FASN 5’-GAACTCCTTGGCGGAAGAGAA-3’ 5’-GCGAGAAGTCAACACGAGCTT-3’ ACLY 5’-AAGATCTCGTGGCCAATGGA-3’ 5’-AGGTTTGCGGATCAAACCAA-3’ ACACA 5’-CTTTGTGCCCACGGTTATCA-3’ 5’-AGTGGTCCCTGTTTGTCTCCA-3’ MDH1 5’-TGCAAGGAAAGGAAGTTGGTG-3’ 5’-TTCGAGCCTTGATGACAGCAG-3’ FADS2 5’ TGGTCATTGACCGCAAGGTT-3’ 5’-AGGCATCCGTTGCATCTTCTC-3’ ME1 5’-GCCATTGTGGTGACTGATGGA-3’ 5’-TCATCCCTCCGCAAGCTGTAT-3’ aP2 5’-GCATGGCCAAACCTAACATGAT-3’ 5’-CCTGGCCCAGTATGAAGGAAA-3’ -actin 5’-CTGTCCACCTTCCAGCAGATGT-3’ 5’-CCTGGCCCAGTATGAAGGAAA-3’ Table S3. The RNAi screen on genes overexpressed in ERBB2-positive breast cancer Accession # Symbol Description Reference shRNA-1* shRNA-2 shRNA-3 % control** ***s.d. z-score % control s.d. z-score % control s.d. z-score NM_006408 AGR2 anterior gradient homolog 2 (Xenopus laevis) 6 65.11 24.59 -1.09 NM_003220 AP2A Transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha) 56 63.64 25.82 -1.15 NM_003222 AP-2 transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma) 56 120.44 13.24 1.43 NM_024320 ATAD4 ATPase family, AAA domain containing 4 6 80.99 10.22 -0.36 NM_005765 ATP6AP2 ATPase, H+ transporting, lysosomal accessory protein 2 6 101.38 20.56 0.56 111.66 45.63 1.03 NM_004888 ATP6V1G1 ATPase, H+ transporting, lysosomal (vacuolar proton pump), member J 6 79.34 8.16 -0.44 88.00 8.47 -0.05 91.86 17.35 0.13 NM_004281 BAG3 BCL2-associated athanogene 3 6 123.59 50.76 1.57 NM_004331 BNIP3L BCL2/adenovirus E1B 19kDa interacting protein 3-like 6 54.62 9.66 -1.61 NM_032937 C9orf37 Chromosome 9 open reading frame 37 6 73.97 14.26 -0.68 75.96 4.18 -0.59 NM_001216 CA9 carbonic anhydrase CA IX 57 54.00 15.87 -1.59 113.45 21.59 1.11 NM_053056 CCND1 cyclin D1 CCND1 58 103.82 36.74 0.67 111.71 17.78 1.03 112.12 12.80 1.05 NM_013230 CD24 CD24 6 95.47 31.12 0.29 NM_004933 CDH15 cadherin 15, M-cadherin (myotubule) CDH15 7 76.98 7.42 -0.55 NM_001793 CDH3 cadherin 3, type 1, P-cadherin (placental) 6 117.26 22.75 1.28 NM_003159 CDLK5 cyclin-dependent kinase-like 5 (CDKL5) 7 79.47 17.01 -0.43 100.02 2.94 0.50 100.25 3.83 0.51 NM_001803 CDW52 CDW52 (CAMPATH-1 antigen) 6 108.56 18.74 0.89 NM_001408 CELSR2 cadherin, EGF LAG seven-pass G-type receptor 2 CELSR2 7 67.39 28.09 -0.98 99.12 9.85 0.46 NM_003909 CPNE3 Copine III 6 68.27 8.09 -0.94 97.32 24.84 0.38 101.69 3.20 0.58 NM_001311 CRIP1 Cysteine-rich protein 1, intestinal 6 109.82 4.13 0.95 NM_024223 CRIP2 cysteine-rich protein 2 6 89.35 24.35 0.02 NM_003651 CSDA Cold shock domain protein A 6 58.04 20.17 -1.41 89.02 3.76 0.00 104.97 13.45 0.73 NM_005213 CSTA cystatin A (stefin A) CSTA 7 72.87 30.71 -0.73 86.53 4.23 -0.11 88.76 3.12 -0.01 NM_005930 CTAGE5 CTAGE family, member 5 (CTAGE5), transcript variant 1 6 107.75 11.03 0.85 NM_001903 CTNNA1 1-Catenin 6 70.10 7.78 -0.86 NM_015462 DKFZP586L0724 DKFZP586L0724 protein 59 97.09 13.30 0.37 99.84 5.44 0.49 100.78 2.70 0.54 NM_004747 DLG5 Discs (Drosophila), large homolog 5 6 97.94 25.44 0.41 NM_005494 DNAJB6 DnaJ (Hsp40) homolog, subfamily B, member 6 6 106.38 6.13 0.79 NM_022365 DNAJC1 DnaJ (Hsp40) homolog, subfamily C, member 1 6 101.86 12.65 0.58 NM_021800 DNAJC12 DnaJ (Hsp40) homolog, subfamily C, member 12 6 87.18 6.46 -0.08 106.17 15.44 0.78 114.95 14.81 1.18 NM_001405 EFNA2 ETS-related transcription factor Elf-1/ephrin-A2 (EFNA2) 60 98.62 19.66 0.44 NM_005228 EGFR epidermal growth factor receptor EGFR 61 67.06 3.17 -1.00 71.46 24.89 -0.80 98.80 20.91 0.45 NM_024757 EHMT1 euchromatic histone-lysine N-methyltransferase 1 (EHMT1) 6 95.40 17.28 0.29 109.08 17.33 0.91 NM_012843 EMP1 epithelial membrane protein 1 6 95.63 37.20 0.30 NM_004901 ENTPD4 ectonucleoside triphosphate diphosphohydrolase 4 (ENTPD4) 6 98.04 2.46 0.41 NM_001429 EP300 ER81 coactivator p300 62 73.43 1.30 -0.71 NM_004448 ERBB2 v-erb-b2 erythroblastic leukemia viral oncogene homolog 2 (avian) 5,6,7 27.03 6.30 -2.82 42.18 6.62 -2.13 48.74 8.93 -1.83 NM_001006600 ERBB2IP erbb2 interacting protein 5 94.51 20.92 0.25 120.82 19.67 1.45 BC082992 ERBB3 v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) 65 69.33 16.86 -0.89 72.18 20.51 -0.76 72.34 0.93 -0.76 NM_000125 ESR1 estrogen receptor 1 ESR1 5, 7 62.29 23.24 -1.21 88.15 15.99 -0.04 91.71 19.06 0.12 NM_004956 ETV1 ETS transcription factor ER81/ets variant gene 1 (ETV1) 62 73.96 4.61 -0.68 92.26 11.39 0.15 105.00 9.21 0.73 NM_178516 EXOC3L exocyst complex component 3-like (loc283849) 7 80.71 1.90 -0.38 81.61 4.20 -0.34 97.27 2.06 0.38 NM_004265 FADS2 fatty acid desaturase 2 FADS2 7 63.55 27.33 -1.16 78.63 4.92 -0.47 86.03 4.08 -0.13 NM_004104 FASN fatty acid synthase FAS 66 75.41 4.15 -0.62 92.39 31.86 0.15 101.57 16.69 0.57 NM_002014 FKBP4 FK506-binding protein 4 6 54.62 4.51 -1.56 91.47 3.12 0.11 106.06 18.86 0.78 NM_004496 FOXA1 Homo sapiens forkhead box A1 (FOXA1) (Hepatocyte nuclear factor 3a) 5 82.08 29.60 -0.31 91.33 1.08 0.11 100.23 22.37 0.51 NM_004483 GCSH glycine cleavage system protein H (aminomethyl carrier) (GCSH) 6 87.16 1.40 -0.08 91.24 23.76 0.10 NM_005310 GRB7 growth factor receptor-bound protein 7 GRB7 5, 59 71.41 0.77 -0.80 76.58 9.95 -0.56 NM_004893 H2AFY H2A histone family, member Y 6 50.47 3.18 -1.75 68.85 19.60 -0.92 NM_005324 H3F3B H3 histone family, 3B 6 70.57 28.50 -0.84 100.91 3.12 0.54 106.72 1.61 0.81 NM_017802 HEATR2 HEAT repeat containing 2 (FLJ20397) 6 62.61 16.34 -1.20 NM_005345 HSPA1A heat shock 70kDa protein 1A 6 75.68 0.97 -0.61 101.02 6.07 0.55 110.94 10.28 1.00 NM_005346 HSPA1B heat shock 70kDa protein 1B 6 107.16 6.13 0.83 NM_005527 HSPA1L heat shock 70kDa protein 1-like 6 95.13 10.70 0.28 NM_002155 HSPA6 heat shock 70kDa protein 6 (HSP70B') (HSPA6) 6 48.23 5.95 -1.85 68.85 22.11 -0.92 70.58 10.38 -0.84 NM_024610 HSPBAP1 HSPB (heat shock 27kDa) associated protein 1 6 87.43 4.73 -0.07 113.28 6.85 1.10 135.30 6.72 2.10 NM_001017963 HSPCA heat shock protein 90kDa alpha (cytosolic), class A member 1 67 94.55 5.29 0.25 NM_007355 HSPCB heat shock protein 90kDa alpha (cytosolic), class B member 1 67 75.67 4.15 -0.61 89.26 1.29 0.01 92.41 5.85 0.16 NM_002203 ITGA2 integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor) ITGA2 7 65.74 31.78 -1.06 80.44 13.43 -0.39 99.28 2.97 0.47 NM_000419 ITGA2B integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B) 7 91.97 11.60 0.13 NM_000212 ITGB3 integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61) ITGB3 7 89.68 10.76 0.03 93.79 14.41 0.22 102.73 24.09 0.62 NM_015202 KIAA0556 KIAA0556 protein 6 79.85 13.40 -0.42 114.45 4.26 1.16 NM_002266 KPNA2 karyopherin alpha 2 (RAG cohort 1, importin alpha 1) 6 78.63 6.77 -0.47 88.94 12.43 0.00 NM_000224 KRT18 Keratin 18 6 89.42 4.25 0.02 126.94 6.36 1.72 NM_005556 KRT7 Keratin 7 5 68.17 2.54 -0.95 NM_006148 LASP1 LIM and SH3 protein 1 59 37.54 15.30 -2.34 43.28 19.44 -2.08 NM_006498 LGALS1 lectin, galactoside-binding, soluble, 2 6 78.79 4.66 -0.46 NM_005570 LMAN1 lectin, mannose-binding, 1 6 86.64 16.09 -0.11 88.32 5.16 -0.03 100.50 6.82 0.52 NM_005574 LMO2 LIM domain only 2 66 67.25 4.93 -0.99 92.05 4.51 0.14 92.99 20.68 0.18 NM_006769 LMO4 LIM domain only 4 LMO4 66 91.97 1.74 0.13 111.19 5.08 1.01 121.30 21.70 1.47 NM_002317 LOX lysyl oxidase LOX 7 77.60 30.62 -0.52 88.35 8.63 -0.03 NM_006726 LRBA LPS-responsive vesicle trafficking, beach and anchor containing LRBA 67 90.99 3.94 0.09 NM_052886 MAL2 T-cell differentiation protein 2 (MAL2) 6 80.80 2.03 -0.37 NM_002758 MAP2K6 mitogen-activated protein kinase kinase 6 MAP2K6 7 37.23 11.97 -2.35 57.00 22.55 -1.45 68.63 3.69 -0.93 NM_005885 MARCH6 membrane-associated ring finger (C3HC4) 6 (MARCH6) 6 54.36 11.40 -1.57 71.29 6.58 -0.80 79.82 4.62 -0.42 NM_032315 MGC4399 Mitochondrial carrier protein 6 99.60 9.64 0.48 96.02 12.64 0.32 NM_033418 MGC9084 chromosome 1 open reading frame 156 (C1orf156) - MGC9084 6 85.82 9.36 -0.14 NM_020300 MGST1 Microsomal glutathione S-transferase 1 6 88.54 0.84 -0.02 110.86 19.34 0.99 NM_002417 MKI67 antigen identified by monoclonal antibody Ki-67 MKI67 7 32.99 5.78 -2.55 61.34 23.85 -1.26 NM_024101 MLPH melanophilin (MLPH) 6 70.55 9.71 -0.84 NM_002421 MMP1 matrix metallopeptidase 1 68 75.25 2.90 -0.62 80.41 8.00 -0.39 NM_033546 MRLC2 Myosin, light polypeptide, regulatory, non-sarcomeric MRLC2 6 81.66 27.47 -0.33 117.07 8.72 1.28 NM_018728 MYO5C myosin VC (MYO5C) 6 84.59 6.56 -0.20 NM_007067 MYST2 MYST histone acetyltransferase 2 (MYST2) 6 99.22 6.64 0.46 103.09 7.75 0.64 120.04 24.70 1.41 NM_000662 NAT1 N-acetyltransferase 1 (arylamine N-acetyltransferase) NAT1 7 138.19 23.72 2.24 NM_001135242 NDRG1 N-myc downstream regulated 1 6 53.95 8.69 -1.59 NM_005005 NDUFB9 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9, 22kDa (NDUFB9) 6 71.44
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