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Table S8: Summary of CN Loss Genes Identified by Fisher Test on SNP-FASST2 Segmentation

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Table S8: Summary of CN Loss Genes identified by Fisher Test on SNP-FASST2 Segmentation Gene Symbol Chromosome Start End Length SLC6A19 chr5 1201709 1225230 23522 SLC6A18 chr5 1225469 1246304 20836 TERT chr5 1253286 1295162 41877 SURF6 chr9 136197551 136203047 5497 MED22 chr9 136207754 136214972 7219 SNORD24 chr9 136216250 136216325 76 RPL7A chr9 136215068 136218280 3213 SNORD36B chr9 136216948 136217019 72 SNORD36A chr9 136217310 136217382 73 SNORD36C chr9 136217700 136217767 68 SURF1 chr9 136218665 136223361 4697 SURF2 chr9 136223420 136228040 4621 SURF4 chr9 136228339 136242970 14632 C9orf96 chr9 136243283 136271220 27938 REXO4 chr9 136271185 136283164 11980 ADAMTS13 chr9 136279458 136324508 45051 CACFD1 chr9 136325086 136335909 10824 SLC2A6 chr9 136336215 136344276 8062 TMEM8C chr9 136379707 136390068 10362 ADAMTSL2 chr9 136397285 136440641 43357 FAM163B chr9 136443536 136445368 1833 DBH chr9 136501484 136524466 22983 SARDH chr9 136528683 136605077 76395 VAV2 chr9 136627015 136857446 230432 LINC00094 chr9 136890560 136896719 6160 BRD3 chr9 136895445 136933141 37697 WDR5 chr9 137001209 137025094 23886 RNU6ATAC chr9 137029561 137029686 126 OLFM1 chr9 137967088 138013030 45943 LOC401557 chr9 138073454 138079152 5699 DDX11L10 chr16 61554 64090 2537 POLR3K chr16 96978 103632 6655 SNRNP25 chr16 103828 107669 3842 RHBDF1 chr16 108057 122629 14573 MPG chr16 127017 135850 8834 NPRL3 chr16 135803 188697 52895 HBZ chr16 202853 204504 1652 HBM chr16 215972 216767 796 HBA2 chr16 222845 223709 865 HBA1 chr16 226678 227520 843 HBQ1 chr16 230332 231178 847 LUC7L chr16 238969 279449 40481 ITFG3 chr16 284800 316119 31320 RGS11 chr16 318309 325914 7606 ARHGDIG chr16 330605 333003 2399 PDIA2 chr16 333117 337209 4093 AXIN1 chr16 337439 402676 65238 MRPL28 chr16 417383 420569 3187 TMEM8A chr16 420775 431950 11176 LOC100134368 chr16 432240 442960 10721 NME4 chr16 447191 450754 3564 DECR2 chr16 451857 462487 10631 RAB11FIP3 chr16 475667 572481 96815 LINC00235 chr16 576846 577407 562 MIR5587 chr16 585315 585368 54 SOLH chr16 577855 604636 26782 MIR3176 chr16 593276 593366 91 C16orf11 chr16 610421 615529 5109 NHLRC4 chr16 617031 619495 2465 PIGQ chr16 619967 634136 14170 RAB40C chr16 639356 679273 39918 WFIKKN1 chr16 681011 684116 3106 C16orf13 chr16 684428 686347 1920 FAM195A chr16 691848 698474 6627 WDR90 chr16 699362 717829 18468 RHOT2 chr16 718082 724174 6093 RHBDL1 chr16 726074 728267 2194 STUB1 chr16 730114 732768 2655 JMJD8 chr16 731666 734439 2774 WDR24 chr16 734701 740400 5700 FBXL16 chr16 742499 755825 13327 METRN chr16 765172 767480 2309 FAM173A chr16 771141 772590 1450 CCDC78 chr16 772581 776473 3893 HAGHL chr16 777265 779715 2451 NARFL chr16 779768 790997 11230 MSLN chr16 810764 818865 8102 MIR662 chr16 820182 820277 96 RPUSD1 chr16 834973 838383 3411 CHTF18 chr16 838621 848074 9454 GNG13 chr16 848040 850733 2694 PRR25 chr16 855442 863861 8420 LMF1 chr16 903634 1031318 127685 SOX8 chr16 1031807 1036979 5173 SSTR5-AS1 chr16 1114081 1128731 14651 SSTR5 chr16 1122755 1131454 8700 C1QTNF8 chr16 1138225 1146244 8020 CACNA1H chr16 1203240 1271772 68533 TPSG1 chr16 1271650 1275254 3605 TPSB2 chr16 1278335 1280185 1851 TPSAB1 chr16 1290677 1292555 1879 TPSD1 chr16 1306272 1308494 2223 UBE2I chr16 1359153 1377019 17867 BAIAP3 chr16 1383605 1399442 15838 TSR3 chr16 1399240 1401873 2634 GNPTG chr16 1401899 1413352 11454 UNKL chr16 1413205 1464705 51501 C16orf91 chr16 1469943 1479345 9403 CCDC154 chr16 1484388 1494490 10103 CLCN7 chr16 1494933 1525085 30153 PTX4 chr16 1535939 1538468 2530 TELO2 chr16 1543351 1560460 17110 TMEM204 chr16 1578741 1605581 26841 IFT140 chr16 1560427 1662109 101683 CRAMP1L chr16 1664640 1727909 63270 HN1L chr16 1728277 1752073 23797 MIR3177 chr16 1784985 1785067 83 MAPK8IP3 chr16 1756220 1820318 64099 NME3 chr16 1820320 1821710 1391 MRPS34 chr16 1821895 1823140 1246 EME2 chr16 1823228 1826239 3012 SPSB3 chr16 1826712 1832581 5870 NUBP2 chr16 1832932 1839192 6261 IGFALS chr16 1840413 1844909 4497 HAGH chr16 1859103 1877195 18093 FAHD1 chr16 1877224 1890203 12980 MEIOB chr16 1883983 1922179 38197 LINC00254 chr16 1928285 1934232 5948 HS3ST6 chr16 1961464 1968231 6768 MSRB1 chr16 1988233 1993294 5062 RPL3L chr16 1994579 2004679 10101 NDUFB10 chr16 2009516 2011976 2461 SNORA10 chr16 2012334 2012467 134 SNORA64 chr16 2012973 2013107 135 RPS2 chr16 2012061 2014827 2767 SNORA78 chr16 2015184 2015311 128 SNHG9 chr16 2014996 2015505 510 RNF151 chr16 2016874 2018976 2103 TBL3 chr16 2022063 2028751 6689 NOXO1 chr16 2028917 2031550 2634 GFER chr16 2034149 2037750 3602 SYNGR3 chr16 2039945 2044276 4332 ZNF598 chr16 2047652 2059822 12171 NPW chr16 2069520 2070756 1237 SLC9A3R2 chr16 2076868 2089027 12160 NTHL1 chr16 2089815 2097867 8053 TSC2 chr16 2097989 2138713 40725 MIR1225 chr16 2140195 2140285 91 PKD1 chr16 2138710 2185899 47190 MIR4516 chr16 2183119 2183205 87 MIR3180-5 chr16 2185977 2186130 154 RAB26 chr16 2198650 2204141 5492 SNORD60 chr16 2205023 2205106 84 TRAF7 chr16 2205798 2228130 22333 THOC6 chr16 3074031 3077756 3726 CCDC64B chr16 3077867 3085542 7676 LOC100128770 chr16 3082481 3089133 6653 MMP25 chr16 3096681 3110724 14044 IL32 chr16 3115312 3119668 4357 TIMP2 chr17 76849058 76921472 72415 LOC100653515 chr17 76886661 76899299 12639 RPTOR chr17 78518624 78940173 421550 CHMP6 chr17 78965640 78973933 8294 BAIAP2-AS1 chr17 79002932 79008519 5588 BAIAP2 chr17 79008946 79091232 82287 MIR657 chr17 79099075 79099173 99 MIR3065 chr17 79099676 79099755 80 MIR338 chr17 79099682 79099749 68 MIR1250 chr17 79106995 79107108 114 AATK chr17 79091095 79139872 48778 AATK-AS1 chr17 79139306 79156964 17659 AZI1 chr17 79163392 79196751 33360 BAHCC1 chr17 79373539 79433358 59820 MIR3186 chr17 79418129 79418214 86 ACTG1 chr17 79476996 79479892 2897 FSCN2 chr17 79495416 79504156 8741 C17orf70 chr17 79506910 79519429 12520 NPLOC4 chr17 79523912 79604138 80227 TSPAN10 chr17 79609348 79615779 6432 PDE6G chr17 79617488 79623607 6120 OXLD1 chr17 79632065 79633618 1554 CCDC137 chr17 79633760 79640936 7177 ARL16 chr17 79648223 79650954 2732 HGS chr17 79650961 79669151 18191 MRPL12 chr17 79670399 79674556 4158 SLC25A10 chr17 79679265 79688046 8782 GCGR chr17 79762009 79771889 9881 FAM195B chr17 79780292 79791167 10876 PPP1R27 chr17 79791367 79792926 1560 P4HB chr17 79801033 79818544 17512 ARHGDIA chr17 79825596 79829282 3687 ALYREF chr17 79845710 79849462 3753 ANAPC11 chr17 79849598 79858363 8766 NPB chr17 79860071 79860781 711 PCYT2 chr17 79860776 79869340 8565 SIRT7 chr17 79869814 79876058 6245 MAFG chr17 79876144 79885587 9444 MAFG-AS1 chr17 79885704 79888629 2926 PYCR1 chr17 79890266 79894968 4703 MYADML2 chr17 79897520 79905109 7590 NOTUM chr17 79910382 79919057 8676 ASPSCR1 chr17 79935425 79975282 39858 STRA13 chr17 79976578 79980785 4208 LRRC45 chr17 79981279 79989027 7749 RAC3 chr17 79989531 79992080 2550 DCXR chr17 79993756 79995573 1818 RFNG chr17 80005777 80009650 3874 GPS1 chr17 80009762 80015346 5585 DUS1L chr17 80015747 80023697 7951 FASN chr17 80036213 80056106 19894 CCDC57 chr17 80059345 80170689 111345 SLC16A3 chr17 80186281 80197375 11095 CSNK1D chr17 80200536 80231594 31059 CD7 chr17 80272745 80275480 2736 SECTM1 chr17 80278899 80291921 13023 TEX19 chr17 80317122 80321652 4531 UTS2R chr17 80332200 80333370 1171 OGFOD3 chr17 80347085 80376513 29429 HEXDC chr17 80376251 80400516 24266 C17orf62 chr17 80400462 80408707 8246 NARF chr17 80416059 80446143 30085 FOXK2 chr17 80477593 80562483 84891 WDR45L chr17 80572437 80606411 33975 RAB40B chr17 80614942 80656598 41657 FN3KRP chr17 80674581 80685893 11313 FN3K chr17 80693451 80709073 15623 ZNF750 chr17 80787309 80797931 10623 TBCD chr17 80709939 80901062 191124 B3GNTL1 chr17 80901666 81009686 108021 METRNL chr17 81037566 81052591 15026 FLJ43681 chr17 81174665 81188573 13909 DGCR6 chr22 18893735 18899601 5867 PRODH chr22 18900286 18924066 23781 DGCR5 chr22 18958010 18982142 24133 DGCR9 chr22 19005346 19007761 2416 DGCR10 chr22 19010136 19011063 928 DGCR11 chr22 19033674 19035888 2215 DGCR2 chr22 19023794 19109967 86174 TSSK2 chr22 19118320 19120136 1817 DGCR14 chr22 19117791 19132190 14400 GSC2 chr22 19136503 19137796 1294 SLC25A1 chr22 19163087 19166338 3252 CLTCL1 chr22 19166986 19279239 112254 Table S8: Summary of CN Loss Genes identified by Fisher Test on SNP-FASST2 Segmentation Name soLute carrier famiLy 6 (neutral amino acid transporter), member 19 soLute carrier famiLy 6, member 18 teLomerase reverse transcriptase surfeit 6 mediator compLex subunit 22 smalL nucLeoLar RNA, C/D box 24 ribosomal protein L7a smalL nucLeoLar RNA, C/D box 36B smalL nucLeoLar RNA, C/D box 36A smalL nucLeoLar RNA, C/D box 36C surfeit 1 surfeit 2 surfeit 4 chromosome 9 open reading frame 96 REX4, RNA exonucLease 4 homoLog (S. cerevisiae) ADAM metalLopeptidase with thrombospondin type 1 motif, 13 calcium channeL fLower domain containing 1 soLute carrier famiLy 2 (faciLitated gLucose transporter), member 6 transmembrane protein 8C ADAMTS-Like 2 famiLy with sequence simiLarity 163, member B dopamine beta-hydroxyLase (dopamine beta-monooxygenase) sarcosine dehydrogenase vav 2 guanine nucLeotide exchange factor Long intergenic non-protein coding RNA 94 bromodomain containing 3 WD repeat domain 5 RNA, U6atac smalL nucLear (U12-dependent spLicing) oLfactomedin 1 uncharacterized LOC401557 DEAD/H (Asp-GLu-ALa-Asp/His) box heLicase 11 Like 10 poLymerase (RNA) III (DNA directed) poLypeptide K, 12.3 kDa smalL nucLear ribonucLeoprotein 25kDa (U11/U12) rhomboid 5 homoLog 1 (DrosophiLa) N-methyLpurine-DNA gLycosyLase nitrogen permease reguLator-Like 3 (S. cerevisiae) hemogLobin, zeta hemogLobin mu chain hemogLobin,
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    Genetics, Development and Cell Biology Publications Genetics, Development and Cell Biology 2020 Building the vertebrate codex using the gene breaking protein trap library Noriko Ichino Mayo Clinic Gaurav K. Varshney National Institutes of Health Ying Wang Iowa State University Hsin-kai Liao Iowa State University Maura McGrail Iowa State University, [email protected] See next page for additional authors Follow this and additional works at: https://lib.dr.iastate.edu/gdcb_las_pubs Part of the Molecular Genetics Commons, and the Research Methods in Life Sciences Commons The complete bibliographic information for this item can be found at https://lib.dr.iastate.edu/ gdcb_las_pubs/261. For information on how to cite this item, please visit http://lib.dr.iastate.edu/howtocite.html. This Article is brought to you for free and open access by the Genetics, Development and Cell Biology at Iowa State University Digital Repository. It has been accepted for inclusion in Genetics, Development and Cell Biology Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Building the vertebrate codex using the gene breaking protein trap library Abstract One key bottleneck in understanding the human genome is the relative under-characterization of 90% of protein coding regions. We report a collection of 1200 transgenic zebrafish strains made with the gene- break transposon (GBT) protein trap to simultaneously report and reversibly knockdown the tagged genes. Protein trap-associated mRFP expression shows previously undocumented expression of 35% and 90% of cloned genes at 2 and 4 days post-fertilization, respectively. Further, investigated alleles regularly show 99% gene-specific mRNA knockdown.
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD

    Supplementary Table S4. FGA Co-Expressed Gene List in LUAD

    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
  • Early Growth Response 1 Regulates Hematopoietic Support and Proliferation in Human Primary Bone Marrow Stromal Cells

    Early Growth Response 1 Regulates Hematopoietic Support and Proliferation in Human Primary Bone Marrow Stromal Cells

    Hematopoiesis SUPPLEMENTARY APPENDIX Early growth response 1 regulates hematopoietic support and proliferation in human primary bone marrow stromal cells Hongzhe Li, 1,2 Hooi-Ching Lim, 1,2 Dimitra Zacharaki, 1,2 Xiaojie Xian, 2,3 Keane J.G. Kenswil, 4 Sandro Bräunig, 1,2 Marc H.G.P. Raaijmakers, 4 Niels-Bjarne Woods, 2,3 Jenny Hansson, 1,2 and Stefan Scheding 1,2,5 1Division of Molecular Hematology, Department of Laboratory Medicine, Lund University, Lund, Sweden; 2Lund Stem Cell Center, Depart - ment of Laboratory Medicine, Lund University, Lund, Sweden; 3Division of Molecular Medicine and Gene Therapy, Department of Labora - tory Medicine, Lund University, Lund, Sweden; 4Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands and 5Department of Hematology, Skåne University Hospital Lund, Skåne, Sweden ©2020 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol. 2019.216648 Received: January 14, 2019. Accepted: July 19, 2019. Pre-published: August 1, 2019. Correspondence: STEFAN SCHEDING - [email protected] Li et al.: Supplemental data 1. Supplemental Materials and Methods BM-MNC isolation Bone marrow mononuclear cells (BM-MNC) from BM aspiration samples were isolated by density gradient centrifugation (LSM 1077 Lymphocyte, PAA, Pasching, Austria) either with or without prior incubation with RosetteSep Human Mesenchymal Stem Cell Enrichment Cocktail (STEMCELL Technologies, Vancouver, Canada) for lineage depletion (CD3, CD14, CD19, CD38, CD66b, glycophorin A). BM-MNCs from fetal long bones and adult hip bones were isolated as reported previously 1 by gently crushing bones (femora, tibiae, fibulae, humeri, radii and ulna) in PBS+0.5% FCS subsequent passing of the cell suspension through a 40-µm filter.