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Supplementary Table 1. Primers for Q-RT-PCR Gene Sequence Product lenght AR CTCACCAAGCTCCTGGACTC 247 AR CAGGCAGAAGACATCTGAAAG 247 ASF1B ACAGGAGTTCATCCGAGTGG 164 ASF1B CCATGTTGTTGTCCCAGTTG 164 CDCA3 CCAAGGAGGAAGCAAGACAG 295 CDCA3 GCTCGTCCTCCAGTTTTCAG 295 DTL AAGTCCGTCATCCCAGACAC 100 DTL TGTGCAGATTTTCCTCATGG 100 ERG TCTTGGACCAACAAGTAGCC 151 ERG GTCGGGATCCGTCATCTTG 151 ETV1 GTTGGGGCATTCAGAAAAAC 165 ETV1 TATCTGGAAAGGCCATGGAG 165 KIAA0101 CTGAAGAGGCAGGAAGCAGT 134 KIAA0101 CCAGGGTAAACAAGGAGACG 134 NUSAP1 AGTTTGTCTCGTCCCCTCAA 167 NUSAP1 CGTTTCTTCCGTTGCTCTTC 167 PSA GCAGCATTGAACCAGAGGAG 393 PSA AGAACTGGGGAGGCTTGAGT 393 TBP GAATATAATCCCAAGCGGTTTG 226 TBP ACTTCACATCACAGCTCCCC 226 UBE2T GTGGACAGAGAAGCATGCAA 208 UBE2T TCACCTTGGCAAAGAACACA 208 Supplementary Table 2. Androgen responsive genes in LNCaP-pcDNA3.1 according to microarray expression analysis Ratio values Official symbol RefSeq Acc# 0nM DHT 1.0nM DHT 10nM DHT 100nM DHT 4h: > 2-fold up-regulated at 4 h FKBP5 NM_004117 1 1.197 1.803 2.229 KCNN2 NM_021614 1 1.307 2.324 2.586 C1orf116 NM_023938 1 1.332 2.467 2.528 TMPRSS2 NM_005656 1 1.632 4.844 6.09 SLC45A3 NM_033102 1 1.63 3.194 3.843 TMEPAI NM_020182 1 1.364 2.197 2.631 KLK2 NM_001002231 1 1.102 2.592 3.08 KCNN2 NM_021614 1 1.435 2.032 2.393 C19orf48 NM_199249 1 1.225 1.876 2.065 C19orf48 NM_199249 1 1.42 2.217 2.325 RTN4 NM_007008 1 1.586 2.054 2.372 NKX3-1 NM_006167 1 1.48 2.972 3.572 LOC400451 NM_207446 1 1.275 1.9 2.033 ZBTB16 NM_001018011 1 2.204 6.005 6.737 TMEPAI NM_020182 1 1.37 3.526 3.973 ZNF187 NM_001023560 1 2.239 2.733 2.288 FAM110B NM_147189 1 1.086 1.725 2.097 GHR NM_000163 1 1.513 1.932 2.02 MBOAT2 NM_138799 1 1.262 1.887 2.056 SGK NM_005627 1 0.961 1.529 2.041 IRS2 NM_003749 1 1.388 1.989 2.519 RHOU NM_021205 1 1.663 3.86 4.136 CLEC2D NM_001004419 1 1.411 2.105 1.745 KLK3 NM_001030047 1 0.966 2.071 2.973 >2-fold downregulated at 4h KCNJ13 NM_002242 1 0.602 0.491 0.537 LDOC1 NM_012317 1 0.505 0.395 0.493 CCDC83 NM_173556 1 0.541 0.485 0.464 C20orf46 NM_018354 1 0.443 0.447 0.488 MT2A NM_005953 1 0.481 0.469 0.567 MT1A NM_005946 1 0.418 0.402 0.517 LCN2 NM_005564 1 0.569 0.504 0.497 DUSP5 NM_004419 1 0.635 0.508 0.48 IGFBP3 NM_000598 1 0.415 0.465 0.491 EFHC2 NM_025184 1 0.491 0.449 0.503 ANXA1 NM_000700 1 0.422 0.357 0.4 SYT11 NM_152280 1 0.471 0.459 0.504 TNNT1 NM_003283 1 0.429 0.426 0.574 PLA2G2A NM_000300 1 0.359 0.341 0.432 MT1G NM_005950 1 0.271 0.261 0.355 BASP1 NM_006317 1 0.562 0.397 0.429 TLL1 NM_012464 1 0.448 0.415 0.536 CP NM_000096 1 0.473 0.425 0.475 TGM3 NM_003245 1 0.578 0.499 0.597 DAPK1 NM_004938 1 0.496 0.41 0.497 SDCBP2 NM_015685 1 0.518 0.493 0.547 SDCBP2 NM_015685 1 0.453 0.414 0.44 MT1X NM_005952 1 0.434 0.407 0.532 PIGR NM_002644 1 0.463 0.469 0.481 LOC440087 NM_001013698 1 0.55 0.5 0.528 S100P NM_005980 1 0.365 0.395 0.411 MT1F NM_005949 1 0.532 0.481 0.605 KLHL1 NM_020866 1 0.457 0.458 0.575 >2-fold upregulated at 24h SORD NM_003104 1 1.439 1.602 2.137 KLK3 NM_001030047 1 0.871 2.533 4.188 PTTG1 NM_004219 1 1.677 2.211 1.751 PSMC4 NM_006503 1 2.017 1.951 1.595 C21orf100 1 1.711 2.023 1.689 RLN1 NM_006911 1 1.67 2.083 2.74 UGT2B17 NM_001077 1 2.422 1.628 0.973 CDC20 NM_001255 1 1.212 2.028 2.336 KCNN2 NM_021614 1 1.207 2.192 3.59 ATP5F1 NM_001688 1 2.042 2.119 2.013 CDCA5 NM_080668 1 1.24 2.936 3.326 MAD2L1 NM_002358 1 1.238 1.984 2.598 TCP1 NM_001008897 1 2.406 2.478 2.326 DC2 NM_021227 1 1.79 1.964 2.16 CENPN NM_018455 1 1.231 2.045 3.903 TMPRSS2 NM_005656 1 0.813 1.358 2.847 DHCR24 NM_014762 1 0.889 1.433 2.243 CDC25A NM_001789 1 1.133 1.714 2.137 SLC45A3 NM_033102 1 0.992 1.509 2.223 PPAPDC1B NM_032483 1 1.624 2.243 2.301 HMBS NM_000190 1 1.837 2.109 2.138 SEMA6A NM_020796 1 2.153 1.744 1.232 FIGNL1 NM_001042762 1 1.584 2.079 1.93 DBI NM_020548 1 1.254 1.692 2.203 HIST1H2AC NM_003512 1 2.074 1.939 1.63 MCM2 NM_004526 1 0.919 1.721 2.074 MCM4 NM_005914 1 1.196 2.362 2.93 PIGW NM_178517 1 1.426 2.035 1.983 TMEPAI NM_020182 1 1.074 1.6 2.728 EHF NM_012153 1 1.961 1.998 2.101 TSC22D1 NM_006022 1 1.861 1.905 2.147 TMSL8 NM_021992 1 1.711 2.198 2.233 PAK1IP1 NM_017906 1 1.303 1.621 2.072 CAPRIN1 NM_005898 1 2.103 1.883 1.618 KLK2 NM_001002231 1 0.995 1.209 2.204 SLC39A6 NM_012319 1 1.739 2.03 2.017 DTL NM_016448 1 0.995 1.963 2.611 CDC2 NM_001786 1 1.904 3.259 2.652 C19orf48 NM_199249 1 0.708 1.237 2.108 LDLR NM_000527 1 1.306 1.645 2.16 CENPM NM_001002876 1 1.09 1.997 2.172 FEN1 NM_004111 1 1.034 1.985 2.133 UGT2B11 NM_001073 1 2.308 1.549 0.928 FBXL17 NM_022824 1 2.438 1.966 1.377 PDIA5 NM_006810 1 1.231 1.761 2.521 TRIP13 NM_004237 1 1.194 1.886 2.153 MCM5 NM_006739 1 1.014 1.659 2.037 NKX3-1 NM_006167 1 1.024 1.624 2.973 SRP9 NM_003133 1 2.345 2.018 1.867 FKBP11 NM_016594 1 1.137 1.634 2.144 CDCA7 NM_031942 1 1.024 1.917 2.658 EPB41L4B NM_018424 1 2.14 1.978 1.679 ID2 NM_002166 1 2.146 1.863 1.915 ACTG1 NM_001614 1 2.364 2.1 1.998 IDH1 NM_005896 1 1.945 2.216 2.343 KIF22 NM_007317 1 1.345 1.775 2.084 CCNB2 NM_004701 1 1.22 2.15 2.182 C1orf43 NM_015449 1 1.963 2.144 2.188 DSEL NM_032160 1 1.437 1.403 2.116 ZBTB16 NM_001018011 1 0.988 1.374 2 MCM7 NM_005916 1 1.085 1.704 2.154 TUBA1A NM_006009 1 2.009 2.196 1.834 NIPSNAP3A NM_015469 1 2.292 1.805 1.22 C7orf24 NM_024051 1 1.54 2.048 2.23 MB NM_005368 1 2.128 2.182 1.715 SLC4A4 NM_003759 1 1.729 2.443 2.795 LEPREL1 NM_018192 1 2.117 1.942 1.657 TMEPAI NM_020182 1 1.138 1.929 3.989 UHRF1 NM_013282 1 1.349 2.633 3.623 LYAR NM_017816 1 1.442 1.923 2.138 TYMS NM_001071 1 1.661 3.74 4.543 NUSAP1 NM_016359 1 1.318 2.7 2.691 PPAP2A NM_003711 1 1.554 2.043 2.198 ID1 NM_002165 1 2.141 1.954 1.656 IL8 NM_000584 1 2.083 2.081 1.8 PASK NM_015148 1 1.282 1.837 2.212 MANEA NM_024641 1 2.333 1.806 1.218 GINS2 NM_016095 1 1.044 2.131 2.798 TMEFF2 NM_016192 1 1.334 2 2.638 FGFR3 NM_000142 1 1.222 1.876 2.211 PCNA NM_002592 1 1.282 1.746 2.464 CCNE2 NM_057735 1 1.601 2.065 1.838 RPL29 NM_000992 1 1.399 1.878 2.178 STT3B NM_178862 1 2.07 2.007 2.071 ATAD2 NM_014109 1 1.577 3.009 3.023 CCT6A NM_001009186 1 2.185 2.319 2.049 CNIH NM_001009551 1 1.934 1.943 2.005 C1orf80 NM_022831 1 2.579 2.395 2.121 CLEC2D NM_001004419 1 1.739 1.306 2.95 TK1 NM_003258 1 1.182 2.315 2.394 SEC11C NM_033280 1 1.238 1.663 2.001 DEGS1 NM_003676 1 1.228 1.729 2.012 UBE2C NM_007019 1 1.334 2.792 2.623 GULP1 NM_016315 1 2.447 2.015 1.693 AADAT NM_016228 1 1.726 2.319 2.856 CACYBP NM_001007214 1 1.91 2.093 2.164 FBXO5 NM_012177 1 1.326 1.933 2.125 MRPL45 NM_032351 1 2.068 2.178 1.921 KLK3 NM_001030047 1 0.809 1.985 2.634 KIAA0101 NM_001029989 1 2.538 4.662 4.382 >2-fold downregulated at 24h LDOC1 NM_012317 1 0.494 0.481 0.475 TNNT1 NM_003283 1 0.444 0.403 0.428 PLA2G2A NM_000300 1 0.241 0.178 0.163 C4orf18 NM_001031700 1 0.763 0.584 0.379 C4orf18 NM_001031700 1 0.998 0.726 0.485 ATP1B1 NM_001001787 1 0.888 0.851 0.467 TLL1 NM_012464 1 0.899 0.682 0.4 PBEF1 NM_005746 1 1.034 0.684 0.487 TGM3 NM_003245 1 0.388 0.355 0.285 SLC30A4 NM_013309 1 0.302 0.244 0.188 OAZ2 NM_002537 1 0.615 0.577 0.498 TFF3 NM_003226 1 0.522 0.493 0.496 LGALS3BP NM_005567 1 0.494 0.462 0.386 S100P NM_005980 1 0.301 0.315 0.327 DHRS3 NM_004753 1 0.439 0.421 0.445 COL5A2 NM_000393 1 0.656 0.554 0.398 ACPP NM_001099 1 0.71 0.584 0.499 RARRES3 NM_004585 1 0.771 0.553 0.48 Supplementary Table 3.
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    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date W O 2017/132291 A l 3 August 2017 (03.08.2017) P O P C T (51) International Patent Classification: [US/US]; 77 Massachusetts Avenue, Cambridge, MA A61K 48/00 (2006.01) C12Q 1/68 (2006.01) 02139 (US). THE GENERAL HOSPITAL CORPORA¬ A61K 39/395 (2006.01) G01N 33/574 (2006.01) TION [US/US]; 55 Fruit Street, Boston, MA 021 14 (US). C12N 15/11 (2006.01) (72) Inventors; and (21) International Application Number: (71) Applicants : REGEV, Aviv [US/US]; 415 Main Street, PCT/US2017/014995 Cambridge, MA 02142 (US). BERNSTEIN, Bradley [US/US]; 55 Fruit Street, Boston, MA 021 14 (US). (22) International Filing Date: TIROSH, Itay [US/US]; 415 Main Street, Cambridge, 25 January 20 17 (25.01 .2017) MA 02142 (US). SUVA, Mario [US/US]; 55 Fruit Street, (25) Filing Language: English Bostn, MA 02144 (US). ROZENBALTT-ROSEN, Orit [US/US]; 415 Main Street, Cambridge, MA 02142 (US). (26) Publication Language: English (74) Agent: NIX, F., Brent; Johnson, Marcou & Isaacs, LLC, (30) Priority Data: 317A East Liberty St., Savannah, GA 31401 (US). 62/286,850 25 January 2016 (25.01.2016) US 62/437,558 2 1 December 201 6 (21. 12.2016) US (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, (71) Applicants: THE BROAD INSTITUTE, INC. [US/US]; AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, 415 Main Street, Cambridge, MA 02142 (US).
  • Adaptive Introgression and De Novo Mutations Increase Access to 2 Novel Fitness Peaks on the Fitness Landscape During a Vertebrate Adaptive Radiation 3 Austin H

    Adaptive Introgression and De Novo Mutations Increase Access to 2 Novel Fitness Peaks on the Fitness Landscape During a Vertebrate Adaptive Radiation 3 Austin H

    1 Supplementary Materials: Adaptive introgression and de novo mutations increase access to 2 novel fitness peaks on the fitness landscape during a vertebrate adaptive radiation 3 Austin H. Patton1,2, Emilie J. Richards1,2, Katelyn J. Gould3, Logan K. Buie3, Christopher H. 4 Martin1,2 5 1Museum of Vertebrate Zoology, University of California, Berkeley, CA 6 2Department of Integrative Biology, University of California, Berkeley, CA 7 3Department of Biology, University of North Carolina at Chapel Hill, NC 8 9 10 Supplementary Methods 11 Sampling of hybrid individuals 12 Samples of hybrid Cyprinodon pupfish included herein were first collected following two 13 separate fitness experiments, conducted on San Salvador Island in 2011 (17) and 2016 (18) 14 respectively. Experiments were carried out in two lakes: Little Lake (LL), and Crescent Pond 15 (CP). Following their initial collection at the conclusion of their respective experiments (see (17) 16 and (18) for protocols), samples were stored in ethanol in C.H.M.’s personal collection. In late 17 2018, 149 hybrid samples were selected for use in this experiment. Of these, 27 are from the 18 experiment conducted in 2011 (14 from LL, 13 from CP), and the remaining 122 are from the 19 2016 experiment (58 from LL, 64 from CP). Due to reduced sample size for some species within 20 Little Lake, we include fish obtained from Osprey Lake for downstream analyses comparing 21 hybrids to Little Lake, as the two comprise a single, interconnected body of water. 22 23 Genomic Library Prep 24 DNA was extracted from the muscle tissue of hybrids using DNeasy Blood and Tissue kits 25 (Qiagen, Inc.); these extractions were then quantified using a Qubit 3.0 fluorometer (Thermo 26 Scientific, Inc).
  • Table SII. Significantly Differentially Expressed Mrnas of GSE23558 Data Series with the Criteria of Adjusted P<0.05 And

    Table SII. Significantly Differentially Expressed Mrnas of GSE23558 Data Series with the Criteria of Adjusted P<0.05 And

    Table SII. Significantly differentially expressed mRNAs of GSE23558 data series with the criteria of adjusted P<0.05 and logFC>1.5. Probe ID Adjusted P-value logFC Gene symbol Gene title A_23_P157793 1.52x10-5 6.91 CA9 carbonic anhydrase 9 A_23_P161698 1.14x10-4 5.86 MMP3 matrix metallopeptidase 3 A_23_P25150 1.49x10-9 5.67 HOXC9 homeobox C9 A_23_P13094 3.26x10-4 5.56 MMP10 matrix metallopeptidase 10 A_23_P48570 2.36x10-5 5.48 DHRS2 dehydrogenase A_23_P125278 3.03x10-3 5.40 CXCL11 C-X-C motif chemokine ligand 11 A_23_P321501 1.63x10-5 5.38 DHRS2 dehydrogenase A_23_P431388 2.27x10-6 5.33 SPOCD1 SPOC domain containing 1 A_24_P20607 5.13x10-4 5.32 CXCL11 C-X-C motif chemokine ligand 11 A_24_P11061 3.70x10-3 5.30 CSAG1 chondrosarcoma associated gene 1 A_23_P87700 1.03x10-4 5.25 MFAP5 microfibrillar associated protein 5 A_23_P150979 1.81x10-2 5.25 MUCL1 mucin like 1 A_23_P1691 2.71x10-8 5.12 MMP1 matrix metallopeptidase 1 A_23_P350005 2.53x10-4 5.12 TRIML2 tripartite motif family like 2 A_24_P303091 1.23x10-3 4.99 CXCL10 C-X-C motif chemokine ligand 10 A_24_P923612 1.60x10-5 4.95 PTHLH parathyroid hormone like hormone A_23_P7313 6.03x10-5 4.94 SPP1 secreted phosphoprotein 1 A_23_P122924 2.45x10-8 4.93 INHBA inhibin A subunit A_32_P155460 6.56x10-3 4.91 PICSAR P38 inhibited cutaneous squamous cell carcinoma associated lincRNA A_24_P686965 8.75x10-7 4.82 SH2D5 SH2 domain containing 5 A_23_P105475 7.74x10-3 4.70 SLCO1B3 solute carrier organic anion transporter family member 1B3 A_24_P85099 4.82x10-5 4.67 HMGA2 high mobility group AT-hook 2 A_24_P101651