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Supplementary file 1B. Differentially expressed genes in cancers compared to non-cancers, ranked according to statistical significance based on features present in all samples in at least one replicate. Acc UGCluster Name Symbol log Fold Changet Adj. P - Value B T57841 Hs.474213 Ubiquitin fusion degradation 1 like (yeast) UFD1L 5,02 5,77E-17 36,61 AA279072 Hs.523875 Inositol polyphosphate phosphatase-like 1 INPPL1 4,29 3,40E-16 34,34 AA454143 Hs.77500 Ubiquitin specific peptidase 4 (proto-oncogene) USP4 5,47 9,11E-16 33,04 N68327 Hs.675604 Transcribed locus 5,16 1,33E-15 32,42 T47230 Hs.522885 Zinc finger protein 32 ZNF32 4,96 3,20E-15 31,39 N95249 Hs.505033 V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog KRAS 5,90 1,30E-14 29,85 R41787 Data not found 3,94 1,30E-14 29,75 H51262 Hs.658489 Chloride channel CLIC-like 1 CLCC1 5,67 3,80E-14 28,60 N74623 Hs.523414 Insulin-like growth factor 2 (somatomedin A) IGF2 8,04 1,04E-13 27,52 AA001614 Data not found 6,13 1,97E-13 26,81 AA488626 Hs.81424 SMT3 suppressor of mif two 3 homolog 1 (S. cerevisiae) SUMO1 6,74 2,96E-13 26,33 N50854 Hs.534334 Nucleolar protein 1, 120kDa NOL1 7,55 4,20E-13 25,91 N54596 Hs.523414 Insulin-like growth factor 2 (somatomedin A) IGF2 6,47 5,33E-12 23,37 AA129397 Hs.522868 Deleted in azoospermia 1 DAZ1 2,09 2,37E-11 21,85 N54596 Hs.523414 Insulin-like growth factor 2 (somatomedin A) IGF2 6,58 2,37E-11 21,78 AA424871 Hs.236646 Transcribed locus 3,00 2,11E-10 19,59 AA446876 Hs.165950 Fibroblast growth factor receptor 4 FGFR4 1,93 5,48E-10 18,59 AA152347 Hs.485557 Glutathione S-transferase A4 GSTA4 -2,38 1,31E-09 17,68 AA598863 Hs.535464 Eukaryotic translation initiation factor 3, subunit C-like EIF3CL 2,02 1,86E-09 17,28 H66005 Data not found 3,87 2,30E-09 17,03 AA677246 Data not found -1,74 3,20E-09 16,65 N47484 Hs.485557 Glutathione S-transferase A4 GSTA4 -2,36 3,50E-09 16,52 AI365391 Hs.153357 Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 PLOD3 1,52 5,02E-09 16,09 AA150422 Hs.221941 Cytochrome b reductase 1 CYBRD1 -2,56 5,02E-09 16,08 AA664101 Hs.76392 Aldehyde dehydrogenase 1 family, member A1 ALDH1A1 -2,87 6,82E-09 15,74 N20305 Hs.20575 Growth arrest-specific 2 like 3 GAS2L3 2,00 9,23E-09 15,40 AA211761 Hs.598634 Transcribed locus -1,69 1,28E-08 15,02 AA482067 Hs.647064 Retinoic acid receptor responder (tazarotene induced) 2 RARRES2 -2,20 1,28E-08 15,00 H77536 Hs.497469 Ethanolamine kinase 2 ETNK2 2,09 1,71E-08 14,68 R70784 Hs.102696 Malignant T cell amplified sequence 1 MCTS1 1,30 1,82E-08 14,59 H01164 Hs.268887 MRNA; cDNA DKFZp686P05119 (from clone DKFZp686P05119) 1,25 1,82E-08 14,56 AA948055 Hs.349283 Chromobox homolog 5 (HP1 alpha homolog, Drosophila) CBX5 1,51 1,84E-08 14,52 AA863125 Hs.112981 DEP domain containing 6 DEPDC6 -1,95 2,02E-08 14,39 AA865224 Hs.709396 Homo sapiens, clone IMAGE:4096273, mRNA -1,30 2,02E-08 14,37 AA858223 Hs.144447 Bromodomain and WD repeat domain containing 2 BRWD2 1,54 2,23E-08 14,24 W49619 Hs.464829 Cadherin 2, type 1, N-cadherin (neuronal) CDH2 -3,06 2,28E-08 14,19 AA417905 Hs.503178 Spectrin, beta, non-erythrocytic 1 SPTBN1 -1,76 2,61E-08 14,03 AA936302 Hs.503178 Spectrin, beta, non-erythrocytic 1 SPTBN1 -1,80 2,81E-08 13,93 R20737 Hs.73625 Kinesin family member 20A KIF20A 1,12 2,88E-08 13,88 H96878 Hs.709414 Transmembrane emp24 protein transport domain containing 4 TMED4 1,10 2,92E-08 13,84 T63980 Hs.632994 MRNA differentially expressed in malignant melanoma, clone MM D3 1,68 3,12E-08 13,75 H19129 Hs.584758 Fibroblast growth factor 12 FGF12 -2,72 3,62E-08 13,58 N69220 Hs.480848 Ubiquitin specific peptidase 38 USP38 1,07 4,13E-08 13,43 R41227 Hs.203965 Putative homeodomain transcription factor 2 PHTF2 1,12 4,85E-08 13,24 AA670419 Hs.592207 Chromosome 22 open reading frame 9 C22orf9 -1,10 4,85E-08 13,22 W67200 Hs.334587 RNA binding protein with multiple splicing RBPMS -1,19 4,98E-08 13,18 W80761 Hs.435413 Metastasis associated 1 family, member 3 MTA3 -1,29 5,27E-08 13,10 AA488297 Hs.595186 Transcribed locus 1,04 5,49E-08 13,04 H90902 Hs.153546 Cell division cycle 23 homolog (S. cerevisiae) CDC23 1,13 8,51E-08 12,58 H17615 Hs.332708 Fibulin 5 FBLN5 -2,56 8,80E-08 12,53 AA199717 Hs.101174 Microtubule-associated protein tau MAPT 1,10 1,17E-07 12,23 AA430504 Hs.93002 Ubiquitin-conjugating enzyme E2C UBE2C 1,53 1,23E-07 12,17 H21943 Data not found 1,76 1,25E-07 12,12 H14208 Hs.631841 Paralemmin PALM -1,44 1,33E-07 12,05 H56345 Hs.709539 Chromosome 19 open reading frame 59 C19orf59 2,64 1,35E-07 12,02 AA490462 Hs.439463 AE binding protein 1 AEBP1 -1,37 1,38E-07 11,97 AA991590 Hs.110675 Apolipoprotein C-I APOC1 -3,26 1,75E-07 11,73 R17667 Hs.706748 Solute carrier family 2 (facilitated glucose transporter), member 1 SLC2A1 1,95 1,99E-07 11,58 H44785 Hs.714159 Transcribed locus 1,23 5,36E-07 10,35 AA004881 Hs.440401 Retinol saturase (all-trans-retinol 13,14-reductase) RETSAT -1,14 5,36E-07 10,34 N30428 Hs.122926 Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid rece NR3C1 0,80 5,36E-07 10,33 AA873159 Hs.110675 Apolipoprotein C-I APOC1 -3,22 5,79E-07 10,24 R54846 Hs.264887 Fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2, Pfe FGFR1 1,45 5,88E-07 10,22 H20543 Hs.6278 Dihydroxyacetone kinase 2 homolog (S. cerevisiae) DAK -1,81 5,98E-07 10,18 R78586 Hs.7753 Transcribed locus 1,27 5,98E-07 10,17 AA034051 Hs.158932 Adenomatous polyposis coli APC 1,05 5,98E-07 10,16 AA873599 Hs.460960 Iduronate 2-sulfatase (Hunter syndrome) IDS 1,61 6,07E-07 10,13 R39446 Hs.714136 Transcribed locus -2,08 6,08E-07 10,12 R85914 Hs.437993 MAM domain containing glycosylphosphatidylinositol anchor 1 MDGA1 1,75 6,25E-07 10,08 R72507 Data not found 0,91 6,32E-07 10,06 H59625 Hs.560373 Transcribed locus 1,27 6,38E-07 10,04 AA142922 Hs.655143 Sorbin and SH3 domain containing 2 SORBS2 -3,04 6,39E-07 10,03 AA598601 Hs.697535 Insulin-like growth factor binding protein 3 IGFBP3 2,15 6,65E-07 9,98 H48148 Hs.4944 Chromosome 9 open reading frame 58 C9orf58 1,91 7,03E-07 9,91 AA443702 Hs.707333 Transcribed locus 1,00 7,16E-07 9,88 H10713 Data not found 1,25 7,28E-07 9,85 N21334 Hs.471156 Abl interactor 2 ABI2 -0,92 7,45E-07 9,82 R42227 Hs.245791 Transcribed locus 0,94 7,90E-07 9,74 R55993 Data not found -1,03 7,90E-07 9,74 R06900 Data not found 1,52 8,21E-07 9,69 R42112 Hs.513856 Candidate tumor suppressor in ovarian cancer 2 DPH1 1,03 8,67E-07 9,63 AA465389 Hs.474781 Neutrophil cytosolic factor 4, 40kDa NCF4 -1,22 8,96E-07 9,58 AA453512 Hs.521954 Transcribed locus, strongly similar to NP_036211.2 diacylglycerol O-acyltransfera -1,21 9,73E-07 9,49 AA521300 Hs.333297 Speckle-type POZ protein-like SPOPL 2,40 1,05E-06 9,41 R33642 Hs.523836 Glutathione S-transferase pi GSTP1 -1,72 1,05E-06 9,39 AA479202 Hs.644633 TIMP metallopeptidase inhibitor 3 (Sorsby fundus dystrophy, pseudoin TIMP3 -2,12 1,17E-06 9,28 H58873 Hs.706748 Solute carrier family 2 (facilitated glucose transporter), member 1 SLC2A1 1,86 1,20E-06 9,24 H22922 Hs.517603 MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase MFNG -1,09 1,20E-06 9,23 R09561 Hs.527653 CD55 molecule, decay accelerating factor for complement (Cromer blo CD55 -1,80 1,37E-06 9,10 R44870 Hs.369606 Cleavage and polyadenylation specific factor 6, 68kDa CPSF6 -1,00 1,48E-06 9,01 AA829294 Hs.437855 RNA polymerase II associated protein 3 RPAP3 1,02 1,88E-06 8,76 AA426516 Hs.645557 Transcribed locus 1,32 1,90E-06 8,74 W74133 Hs.47125 GINS complex subunit 3 (Psf3 homolog) GINS3 1,13 1,97E-06 8,70 AA449715 Hs.15154 Sushi-repeat-containing protein, X-linked SRPX -1,29 2,10E-06 8,63 N95578 Hs.535801 CDNA clone IMAGE:4346813 1,04 2,25E-06 8,55 AA485893 Hs.78224 Ribonuclease, RNase A family, 1 (pancreatic) RNASE1 -2,26 2,30E-06 8,52 R33439 Hs.24640 Semaphorin 7A, GPI membrane anchor (John Milton Hagen blood grou SEMA7A 1,20 2,30E-06 8,50 AA701963 Hs.521212 Aldo-keto reductase family 1, member B1 (aldose reductase) AKR1B1 -2,69 2,30E-06 8,50 N54296 Hs.94949 Methylmalonyl CoA epimerase MCEE -0,74 2,30E-06 8,49 R56149 Hs.533336 BMP and activin membrane-bound inhibitor homolog (Xenopus laevis) BAMBI -1,00 2,30E-06 8,49 H14810 Data not found 1,43 2,32E-06 8,47 AA461071 Hs.516866 Solute carrier family 23 (nucleobase transporters), member 2 SLC23A2 -1,81 2,36E-06 8,44 W74668 Hs.59138 Glycophorin C (Gerbich blood group) GYPC -1,21 2,39E-06 8,42 H81645 Hs.162877 Protein kinase C and casein kinase substrate in neurons 2 PACSIN2 -1,18 2,54E-06 8,35 R55294 Data not found -1,82 2,65E-06 8,30 AA457728 Data not found 1,01 2,80E-06 8,24 AA406231 Hs.712560 Dishevelled associated activator of morphogenesis 2 DAAM2 -2,09 2,81E-06 8,23 AA465381 Hs.632527 Solute carrier family 35, member F5 SLC35F5 -1,11 3,02E-06 8,15 AA451851 Hs.102735 Single-stranded DNA binding protein 2 SSBP2 1,47 3,18E-06 8,09 AI361330 Hs.469030 Methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, me MTHFD2 1,15 3,23E-06 8,06 AA465663 Hs.654395 Fc fragment of IgG, low affinity IIb, receptor (CD32) FCGR2B -1,08 3,23E-06 8,05 H98241 Hs.503178 Spectrin, beta, non-erythrocytic 1 SPTBN1 -1,84 3,23E-06 8,05 R07607 Hs.349283 Chromobox homolog 5 (HP1 alpha homolog, Drosophila) CBX5 0,99 3,48E-06 7,97 N48827 Hs.467524 Ubiquitin specific peptidase 48 USP48 -1,16 3,50E-06 7,96 R51912 Hs.12409 Somatostatin SST 0,93 3,51E-06 7,95 T72259 Data not found 1,59 3,51E-06 7,94 AA683321 Hs.664675 Prader-Willi/Angelman syndrome-5 PAR5 1,29 3,51E-06 7,93 R07296 Hs.496383 Sterol O-acyltransferase (acyl-Coenzyme A: cholesterol acyltransferas SOAT1 -1,72 3,75E-06 7,86 AA678159 Hs.563228 Transcribed locus -2,13 3,76E-06 7,85 AA757678 Data not found 1,17 8,09E-06
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    Immunity, Volume 38 Supplemental Information IRF4 Transcription Factor-Dependent CD11b+ Dendritic Cells in Human and Mouse Control Mucosal IL-17 Cytokine Responses Andreas Schlitzer, Naomi McGovern, Pearline Teo, Teresa Zelante, Koji Atarashi, Donovan Low, Adrian W.S. Ho, Peter See, Amanda Shin, Pavandip Singh Wasan, Guillaume Hoeffel, Benoit Malleret, Alexander Heiseke, Samantha Chew, Laura Jardine, Harriet A. Purvis, Catharien M.U. Hilkens, John Tam, Michael Poidinger, E. Richard Stanley, Anne B. K rug, Laurent Renia, Baalasubramanian Sivasankar, Lai Guan Ng, Matthew Collin, Paola Ricciardi-Castagnoli, Kenya Honda, Muzlifah Haniffa, and Florent Ginhoux Supplemental Inventory 1. Supplemental Figures and Tables Figure S1, Related to Figure 1 Figure S2, Related to Figure 2 and 3 Figure S3, Related to Figure 4 Figure S4, Related to Figure 5 Figure S5, Related to Figure 5 Figure S6, Related to Figure 7 Table S1, Related to Figure 3 Table S2, Related to Figure 6 Table S3, Related to Figure 6 2. Supplemental Experimental Procedures 3. Supplemental References Supplementary figure 1 Sorting strategy for mouse lung and small intestinal DC A Sorting strategy, Lung Singlets Dapi-CD45+ 250K 250K 250K 105 200K 200K 200K 104 A I - 150K 150K 150K C P C C 3 10 S A S S 100K 100K S 100K D S S 102 50K 50K 50K 0 0 0 0 0 50K 100K 150K 200K 250K 0 50K 100K 150K 200K 250K 0 103 104 105 0 103 104 105 FSC FSC-W CD45 GR1 Auto Fluor.- MHCII+ GR1- SSClow CD11c+ CD11b+ 250K 105 105 105 200K 4 104 10 104 150K I 3 I 3 4 3 0 10 3 C 2 H 10 10 100K 1 S D C D S C M 2 C 10 50K 0 0 0 0 0 102 103 104 105 0 103 104 105 0 103 104 105 0 103 104 105 Auto fluor.
  • A Human Population-Based Organotypic in Vitro Model for Cardiotoxicity Screening1

    A Human Population-Based Organotypic in Vitro Model for Cardiotoxicity Screening1

    ALTEX preprint published July 8, 2018 doi:10.14573/altex.1805301 Research Article A human population-based organotypic in vitro model for cardiotoxicity screening1 Fabian A. Grimm1, Alexander Blanchette1, John S. House2, Kyle Ferguson1, Nan-Hung Hsieh1, Chimeddulam Dalaijamts1, Alec A. Wright1, Blake Anson5, Fred A. Wright3,4, Weihsueh A. Chiu1, Ivan Rusyn1 1Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA; 2Bioinformatics Research Center, 3Department of Biological Sciences, and 4Department of Statistics, North Carolina State University, Raleigh, NC, USA; 5Cellular Dynamics International, Madison, WI, USA Abstract Assessing inter-individual variability in responses to xenobiotics remains a substantial challenge, both in drug development with respect to pharmaceuticals and in public health with respect to environmental chemicals. Although approaches exist to characterize pharmacokinetic variability, there are no methods to routinely address pharmacodynamic variability. In this study, we aimed to demonstrate the feasibility of characterizing inter-individual variability in a human in vitro model. Specifically, we hypothesized that genetic variability across a population of iPSC- derived cardiomyocytes translates into reproducible variability in both baseline phenotypes and drug responses. We measured baseline and drug-related effects in iPSC-derived cardiomyocytes from 27 healthy donors on kinetic Ca2+ flux and high-content live cell imaging. Cells were treated in concentration-response with cardiotoxic drugs: isoproterenol (β- adrenergic receptor agonist/positive inotrope), propranolol (β-adrenergic receptor antagonist/negative inotrope), and cisapride (hERG channel inhibitor/QT prolongation). Cells from four of the 27 donors were further evaluated in terms of baseline and treatment-related gene expression. Reproducibility of phenotypic responses was evaluated across batches and time.
  • Functional Genomics Atlas of Synovial Fibroblasts Defining Rheumatoid Arthritis

    Functional Genomics Atlas of Synovial Fibroblasts Defining Rheumatoid Arthritis

    medRxiv preprint doi: https://doi.org/10.1101/2020.12.16.20248230; this version posted December 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability Xiangyu Ge1*, Mojca Frank-Bertoncelj2*, Kerstin Klein2, Amanda Mcgovern1, Tadeja Kuret2,3, Miranda Houtman2, Blaž Burja2,3, Raphael Micheroli2, Miriam Marks4, Andrew Filer5,6, Christopher D. Buckley5,6,7, Gisela Orozco1, Oliver Distler2, Andrew P Morris1, Paul Martin1, Stephen Eyre1* & Caroline Ospelt2*,# 1Versus Arthritis Centre for Genetics and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK 2Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland 3Department of Rheumatology, University Medical Centre, Ljubljana, Slovenia 4Schulthess Klinik, Zurich, Switzerland 5Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK 6NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, Birmingham, UK 7Kennedy Institute of Rheumatology, University of Oxford Roosevelt Drive Headington Oxford UK *These authors contributed equally #corresponding author: [email protected] NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. 1 medRxiv preprint doi: https://doi.org/10.1101/2020.12.16.20248230; this version posted December 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
  • Genetic Landscape of Papillary Thyroid Carcinoma and Nuclear Architecture: an Overview Comparing Pediatric and Adult Populations

    Genetic Landscape of Papillary Thyroid Carcinoma and Nuclear Architecture: an Overview Comparing Pediatric and Adult Populations

    cancers Review Genetic Landscape of Papillary Thyroid Carcinoma and Nuclear Architecture: An Overview Comparing Pediatric and Adult Populations 1, 2, 2 3 Aline Rangel-Pozzo y, Luiza Sisdelli y, Maria Isabel V. Cordioli , Fernanda Vaisman , Paola Caria 4,*, Sabine Mai 1,* and Janete M. Cerutti 2 1 Cell Biology, Research Institute of Oncology and Hematology, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada; [email protected] 2 Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo/EPM, São Paulo, SP 04039-032, Brazil; [email protected] (L.S.); [email protected] (M.I.V.C.); [email protected] (J.M.C.) 3 Instituto Nacional do Câncer, Rio de Janeiro, RJ 22451-000, Brazil; [email protected] 4 Department of Biomedical Sciences, University of Cagliari, 09042 Cagliari, Italy * Correspondence: [email protected] (P.C.); [email protected] (S.M.); Tel.: +1-204-787-2135 (S.M.) These authors contributed equally to this paper. y Received: 29 September 2020; Accepted: 26 October 2020; Published: 27 October 2020 Simple Summary: Papillary thyroid carcinoma (PTC) represents 80–90% of all differentiated thyroid carcinomas. PTC has a high rate of gene fusions and mutations, which can influence clinical and biological behavior in both children and adults. In this review, we focus on the comparison between pediatric and adult PTC, highlighting genetic alterations, telomere-related genomic instability and changes in nuclear organization as novel biomarkers for thyroid cancers. Abstract: Thyroid cancer is a rare malignancy in the pediatric population that is highly associated with disease aggressiveness and advanced disease stages when compared to adult population.
  • Rabbit Anti-DAZAP1/FITC Conjugated Antibody-SL14200R-FITC

    Rabbit Anti-DAZAP1/FITC Conjugated Antibody-SL14200R-FITC

    SunLong Biotech Co.,LTD Tel: 0086-571- 56623320 Fax:0086-571- 56623318 E-mail:[email protected] www.sunlongbiotech.com Rabbit Anti-DAZAP1/FITC Conjugated antibody SL14200R-FITC Product Name: Anti-DAZAP1/FITC Chinese Name: FITC标记的无精症缺失相关蛋白1抗体 DAZ associated protein 1; DAZ-associated protein 1; Dazap1; DAZP1_HUMAN; Alias: Deleted in azoospermia associated protein 1; Deleted in azoospermia-associated protein 1. Organism Species: Rabbit Clonality: Polyclonal React Species: Human,Mouse,Rat,Chicken,Dog,Pig,Cow,Horse,Sheep, ICC=1:50-200IF=1:50-200 Applications: not yet tested in other applications. optimal dilutions/concentrations should be determined by the end user. Molecular weight: 43kDa Form: Lyophilized or Liquid Concentration: 1mg/ml immunogen: KLH conjugated synthetic peptide derived from human DAZAP1 Lsotype: IgG Purification: affinity purified by Protein A Storage Buffer: 0.01Mwww.sunlongbiotech.com TBS(pH7.4) with 1% BSA, 0.03% Proclin300 and 50% Glycerol. Store at -20 °C for one year. Avoid repeated freeze/thaw cycles. The lyophilized antibody is stable at room temperature for at least one month and for greater than a year Storage: when kept at -20°C. When reconstituted in sterile pH 7.4 0.01M PBS or diluent of antibody the antibody is stable for at least two weeks at 2-4 °C. background: In mammals, the Y chromosome directs the development of the testes and plays an important role in spermatogenesis. A high percentage of infertile men have deletions that map to regions of the Y chromosome. The DAZ (deleted in azoospermia) gene Product Detail: cluster maps to the AZFc region of the Y chromosome and is deleted in many azoospermic and severely oligospermic men.