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Supplementary Table 4: Genes Down- and Up-Regulated After Culture in KSOM Vs VIVO

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Supplementary table 4: Genes down- and up-regulated after culture in KSOM vs VIVO Fold change Gene symbol Description Affymetrix number -20.25 Rassf4 Ras association (RalGDS/AF-6) domain family 4 1444009_at -14.06 Bhmt2 betaine-homocysteine methyltransferase 2 1418914_s_at -10.56 Akp5 alkaline phosphatase 5 1450635_at -7.02 Socs3 suppressor of cytokine signaling 3 1455899_x_at -5.76 Nucb2 nucleobindin 2 1418355_at -5.76 Stmn3 stathmin-like 3 1435113_x_at -5.29 Bhmt betaine-homocysteine methyltransferase 1450624_at -5.29 Akr1c21 aldo-keto reductase family 1, member C21 1451030_at -5.06 Bmp4 bone morphogenetic protein 4 1422912_at -4.62 Fgf4 fibroblast growth factor 4 1420085_at -4.62 Cbfa2t1h CBFA2T1 identified gene homolog (human) 1444615_x_at -4.41 Arf7 ADP-ribosylation factor 7 1430234_at -4.20 Tmem64 transmembrane protein 64 1434307_at -4.20 Cpxm1 carboxypeptidase X 1 (M14 family) 1448901_at -4.20 Apcdd1 adenomatosis polyposis coli down-regulated 1 1454822_x_at -4.00 Dmgdh dimethylglycine dehydrogenase precursor 1452311_at -3.61 Morc1 microrchidia 1 1419418_a_at -3.61 Tmem64 transmembrane protein 64 1433735_a_at -3.61 Parvb Parvin, beta (Parvb), mRNA 1438672_at -3.61 Akp5 alkaline phosphatase 5 1450636_s_at -3.42 Cebpa CCAAT/enhancer binding protein (C/EBP), alpha 1418982_at -3.24 --- Transcribed locus 1448021_at -3.06 Snap91 synaptosomal-associated protein 91 1416688_at -2.89 MGI:1919030 myo-inositol 1-phosphate synthase A1 1415977_at -2.89 --- RNA transcript from U17 small nucleolar RNA host gene 1433789_at -2.56 Tspan1 tetraspan 1 1417957_a_at -2.56 4921530G04Rik RIKEN cDNA 4921530G04 gene 1460274_at -2.40 Tcl1 T-cell lymphoma breakpoint 1 1422458_at -2.40 Fasn fatty acid synthase 1423828_at -2.25 Tex19 testis expressed gene 19 1417482_at -2.25 Ube2a ubiquitin-conjugating enzyme E2A, RAD6 homolog (S. cerevisiae) 1417609_at -2.25 Tmepai transmembrane, prostate androgen induced RNA 1422706_at -2.25 Pnliprp2 pancreatic lipase-related protein 2 1437438_x_at -1.96 Wrnip1 Werner helicase interacting protein 1 1448376_at -1.82 Sox2 SRY-box containing gene 2 1416967_at -1.82 Pias2 protein inhibitor of activated STAT 2 1428725_at -1.82 Cxxc6 CXXC finger 6 1429448_s_at -1.82 Tmcc3 transmembrane and coiled coil domains 3 1435554_at -1.82 Slc16a10 solute carrier family 16 (monocarboxylic acid transporters), member 10 1436368_at -1.82 Rrbp1 ribosome binding protein 1 1449221_a_at -1.69 Fscn1 fascin homolog 1, actin bundling protein (Strongylocentrotus) purpuratus) 1416514_a_at -1.69 Glt28d1 glycosyltransferase 28 domain containing 1 1418681_at -1.69 Kcmf1 potassium channel modulatory factor 1 1418694_at -1.69 Rpl13a ribosomal protein L13a 1433928_a_at -1.69 Lhfpl2 lipoma HMGIC fusion partner-like 2 1434129_s_at -1.69 --- Mus musculus, clone IMAGE:4219318, mRNA 1442003_at -1.69 Upp1 uridine phosphorylase 1 1448562_at -1.69 Ssx2ip synovial sarcoma, X breakpoint 2 interacting protein 1448743_at -1.69 D11Ertd759e DNA segment, Chr 11, ERATO Doi 759, expressed 1455500_at -1.56 Tpst1 protein-tyrosine sulfotransferase 1 1421733_a_at -1.56 Rpl5 ribosomal protein L5 /// similar to 60S ribosomal protein L5 /// similar to 60S ribosomal protein L5 1423666_s_at -1.56 S100a16 S100 calcium binding protein A16 1425560_a_at -1.56 Wdr40b WD repeat domain 40B 1434170_at -1.56 2310007O11Rik RIKEN cDNA 2310007O11 gene 1436446_at -1.56 Map4k4 mitogen-activated protein kinase 4 1448050_s_at -1.56 Ddx21 DEAD (Asp-Glu-Ala-Asp) box polypeptide 21 1448271_a_at -1.56 Pycr2 pyrroline-5-carboxylate reductase family, member 2 1448315_a_at -1.56 5730557B15Rik RIKEN cDNA 5730557B15 gene 1453287_at -1.56 Wdr6 WD repeat domain 6 1455940_x_at -1.56 Ccbl2 cysteine conjugate-beta lyase 2 1455991_at -1.44 Scd2 stearoyl-Coenzyme A desaturase 2 1415824_at -1.44 Satb1 special AT-rich sequence binding protein 1 1416007_at -1.44 Gclc glutamate-cysteine ligase, catalytic subunit 1424296_at -1.44 Phf3 PHD finger protein 3 1429000_at -1.44 Eomes eomesodermin homolog (Xenopus laevis) 1435172_at -1.44 Pfkl phosphofructokinase, liver, B-type 1439148_a_at -1.44 Chka choline kinase alpha 1450264_a_at -1.44 Ckb creatine kinase, brain 1455106_a_at -1.44 LOC545325 hypothetical protein LOC545325 1455604_at -1.44 Dus3l dihydrouridine synthase 3-like (S. cerevisiae) 1459805_x_at -1.32 Sms spermine synthase 1421052_a_at -1.32 Slc25a20 solute carrier family 25 (mitochondrial carnitine/acylcarnitine translocase), member 20 1423108_at -1.32 Ldlrap1 low density lipoprotein receptor adaptor protein 1 1424378_at -1.32 4121402D02Rik RIKEN cDNA 4121402D02 gene 1428873_a_at -1.32 D6Ertd253e DNA segment, Chr 6, ERATO Doi 253, expressed 1433509_s_at -1.32 Dpp7 dipeptidylpeptidase 7 1436479_a_at -1.32 Kpnb1 karyopherin (importin) beta 1 1448526_at -1.32 Usp25 ubiquitin specific peptidase 25 1448939_at -1.32 BB001228 expressed sequence BB001228 1455425_at -1.21 Oact2 O-acyltransferase (membrane bound) domain containing 2 1425029_a_at -1.21 9430034D17Rik RIKEN cDNA 9430034D17 gene, mRNA (cDNA clone IMAGE:30109386) 1434398_at -1.21 --- --- 1440253_at -1.21 Tial1 Tial1 cytotoxic granule-associated RNA binding protein-like 1 1452821_at -1.21 BC021395 cDNA sequence BC021395 1454964_at -1.10 Nfxl1 nuclear transcription factor, X-box binding-like 1 1417145_at -1.10 Klf4 Kruppel-like factor 4 (gut) 1417394_at -1.10 Dgat1 diacylglycerol O-acyltransferase 1 1418295_s_at -1.10 0610039J04Rik RIKEN cDNA 0610039J04 gene 1428798_s_at -1.10 Tmem57 transmembrane protein 57 1428883_at -1.10 Sema5a sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) 1437422_at -1.10 --- --- 1438962_s_at -1.10 4930453N24Rik RIKEN cDNA 4930453N24 gene 1449718_s_at -1.10 Tdgf1 teratocarcinoma-derived growth factor 1450989_at -1.10 Pten phosphatase and tensin homolog 1455728_at -1.00 Trrap transformation/transcription domain-associated protein 1416532_at -1.00 Rpl22l1 ribosomal protein L22 like 1 1417126_a_at -1.00 Rpl14 ribosomal protein L14 1422128_at -1.00 4930517K11Rik RIKEN cDNA 4930517K11 gene 1423327_at -1.00 2700078E11Rik RIKEN cDNA 2700078E11 gene 1424983_a_at -1.00 Eomes eomesodermin homolog (Xenopus laevis) 1426001_at -1.00 Axin1 axin 1 1426966_at -1.00 Nfx1 nuclear transcription factor, X-box binding 1 1428248_at -1.00 1300004G08Rik RIKEN cDNA 1300004G08 gene /// similar to hypothetical protein LOC65259 1428565_at -1.00 --- --- 1429321_at -1.00 Cct4 chaperonin subunit 4 (delta) 1430034_at -1.00 6720458F09Rik RIKEN cDNA 6720458F09 gene 1433962_at -1.00 Cds2 CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2 1434256_s_at -1.00 1110064P04Rik RIKEN cDNA 1110064P04 gene 1435160_at -1.00 Phtf2 putative homeodomain transcription factor 2 1437067_at -1.00 Noc4l nucleolar complex associated 4 homolog (S. cerevisiae) 1443794_x_at -1.00 Akap1 A kinase (PRKA) anchor protein 1 1449019_at -1.00 Fxr1h fragile X mental retardation gene 1, autosomal homolog 1452247_at -0.90 Ncl nucleolin 1415772_at -0.90 Crip1 cysteine-rich protein 1 (intestinal) 1416326_at -0.90 Surf6 surfeit gene 6 1416864_at -0.90 Npepps aminopeptidase puromycin sensitive 1417385_at -0.90 Epb4.1l4b erythrocyte protein band 4.1-like 4b 1418294_at -0.90 D11Ertd707e DNA segment, Chr 11, ERATO Doi 707, expressed 1418543_s_at -0.90 Smad4 MAD homolog 4 (Drosophila) 1422486_a_at -0.90 0610039J04Rik RIKEN cDNA 0610039J04 gene 1428797_at -0.90 Tor2a torsin family 2, member A 1438547_x_at -0.90 Gna13 guanine nucleotide binding protein, alpha 13 1450656_at -0.90 Wdr79 WD repeat domain 79 1456724_x_at -0.90 Chordc1 cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1 1460645_at -0.81 Gna13 guanine nucleotide binding protein, alpha 13 1422555_s_at -0.81 D10Ucla1 DNA segment, Chr 10, University of California at Los Angeles 1 1424780_a_at -0.81 Etv5 ets variant gene 5 1428142_at -0.81 AU020206 expressed sequence AU020206 1433935_at -0.81 Dhps deoxyhypusine synthase 1434003_a_at -0.81 Gprk6 G protein-coupled receptor kinase 6 1437436_s_at -0.81 AI326906 Nucleolar complex associated 4 homolog (S. cerevisiae) (Noc4l), mRNA 1438095_x_at -0.81 Htra1 HtrA serine peptidase 1 1438251_x_at -0.81 Nuak1 ZNUAK family, SNF1-like kinase, 1 1438684_at -0.81 Cds2 CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2 1438957_x_at -0.81 Srpk1 serine/arginine-rich protein specific kinase 1 1455107_at -0.81 Chd1 chromodomain helicase DNA binding protein 1 1457473_at -0.72 Etv3 ets variant gene 3 1418635_at -0.72 LOC433829 similar to Piwi/Argonaute family protain meIF2C1 1434331_at -0.72 BC005537 cDNA sequence BC005537 1423154_at -0.72 Gnpnat1 glucosamine-phosphate N-acetyltransferase 1 1423158_at -0.72 Ddx26 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26 1423275_at -0.72 Ubxd4 UBX domain containing 4 1425019_at -0.72 Narg1l NMDA receptor regulated 1-like 1429057_at -0.72 Kbtbd8 kelch repeat and BTB (POZ) domain containing 8 1433902_at -0.72 Ampd2 adenosine monophosphate deaminase 2 (isoform L) 1438941_x_at -0.72 Tnks2 tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2 1447522_s_at -0.72 Usp10 ubiquitin specific peptidase 10 1448230_at -0.72 Picalm phosphatidylinositol binding clathrin assembly protein 1451316_a_at -0.72 Hspa1a heat shock protein 1A 1452318_a_at -0.72 Cggbp1 CGG triplet repeat binding protein 1 1454641_at -0.72 Ibtk inhibitor of Bruton agammaglobulinemia tyrosine kinase 1454905_at -0.72 Grwd1 glutamate-rich WD repeat containing 1 1455841_s_at -0.64 1110005A23Rik RIKEN cDNA 1110005A23 gene 1416095_x_at -0.64 Htra1 HtrA serine peptidase 1 1416749_at -0.64 Dnajb1 DnaJ (Hsp40) homolog,
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    Linköping University Medical Dissertations No. 1158 Antigen interaction with B cells in two proliferative disorders - CLL and MGUS Eva Hellqvist Akademisk avhandling som för avläggande av medicine doktorsexamen offentligen försvaras i Aulan, Katastrofmedicinskt Centrum, Linköping, fredagen den 15 januari 2010 kl. 9.00 Fakultetsopponent Dr Anne Mette Buhl Department of Hematology, Rigshospitalet Copenhagen, Denmark Division of Cell Biology Department of Clinical and Experimental Medicine Linköping University, SE-581 85 Linköping, Sweden Linköping 2010 All text, tables and illustrations are © Eva Hellqvist, 2010 The original papers included in this thesis have been reprinted with the permission of respective copyright holder: Paper I: © the American Society of Hematology Paper IV: © the Ferrata Storti Foundation ISSN: 0345-0082 ISBN: 978-91-7393-475-6 Printed in Sweden by LiU-Tryck, Linköping 2010 “This world, after all our science and sciences, is still a miracle; wonderful, inscrutable, magical and more, to whosoever will think of it. ” – Thomas Carlyle TO MY GREAT SURPRISE SUPERVISOR Anders Rosén, Professor Division of Cell Biology Department of Clinical and Experimental Medicine Linköping University, Sweden CO-SUPERVISOR Jan Ernerudh, Professor Division of Clinical Immunology Department of Clinical and Experimental Medicine Linköping University, Sweden OPPONENT Anne Mette Buhl, Associate Professor Department of Hematology Rigshospitalet Copenhagen, Denmark COMMITTEE BOARD Hodjattalah Rabbani, Associate Professor Immune and Gene Therapy
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    Hypoxia-Inducible Factor Regulates Survival of Antigen Receptor-Driven T Cells Yuichi Makino, Hiroshi Nakamura, Eiji Ikeda, Kei Ohnuma, Kenji Yamauchi, Yutaka Yabe, Lorenz Poellinger, Yasunori This information is current as Okada, Chikao Morimoto and Hirotoshi Tanaka of September 28, 2021. J Immunol 2003; 171:6534-6540; ; doi: 10.4049/jimmunol.171.12.6534 http://www.jimmunol.org/content/171/12/6534 Downloaded from References This article cites 46 articles, 17 of which you can access for free at: http://www.jimmunol.org/content/171/12/6534.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication by guest on September 28, 2021 *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2003 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Hypoxia-Inducible Factor Regulates Survival of Antigen Receptor-Driven T Cells1 ‡,Kenji Yamauchi ء,Eiji Ikeda,† Kei Ohnuma ء,Hiroshi Nakamura ء,Yuichi Makino and ء,Yutaka Yabe,‡ Lorenz Poellinger,§ Yasunori Okada,† Chikao Morimoto ءHirotoshi Tanaka2 Peripheral T lymphocytes undergo activation by antigenic stimulation and function in hypoxic areas of inflammation.