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Table S-1 Mpkccd Transcriptome

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Table S1. mpkCCD Cell Transcriptomes. Correlati on Ori. Ratio Coefficie Gene Symbol Gene Title GeneID Clone 11 Clone Clone 2 (11/2) nt Copg coatomer protein complex, subunit gamma 54161 1.99 1.81 2.48 0.80 -0.49 ns Atp6v0d1 ATPase, H+ transporting, lysosomal V0 subunit D1 11972 3.37 2.87 3.00 1.12 0.74 ns Golga7 golgi autoantigen, golgin subfamily a, 7 57437 3.03 3.40 3.58 0.84 -0.34 ns Psph phosphoserine phosphatase 100678 0.38 0.66 0.64 0.59 -0.61 ns Trappc4 trafficking protein particle complex 4 60409 1.17 1.12 1.08 1.08 0.64 ns Dpm2 dolichol-phosphate (beta-D) mannosyltransferase 2 13481 0.74 0.87 0.81 0.91 -0.31 ns Psmb5 proteasome (prosome, macropain) subunit, beta type 5 19173 2.92 3.00 2.92 0.99 0.32 ns Dhrs1 dehydrogenase/reductase (SDR family) member 1 52585 0.74 0.68 0.88 0.83 -0.18 ns Ppm1a protein phosphatase 1A, magnesium dependent, alpha isoform 19042 2.43 2.60 2.96 0.82 -0.53 ns Psenen presenilin enhancer 2 homolog (C. elegans) 66340 2.52 2.88 3.80 0.66 -0.77 ns Anapc1 anaphase promoting complex subunit 1 17222 1.16 1.33 1.61 0.72 -0.33 ns Mrpl43 mitochondrial ribosomal protein L43 94067 2.15 2.15 1.84 1.16 0.91 * Nmt1 N-myristoyltransferase 1 18107 3.21 2.71 3.36 0.95 0.31 ns Atg5 autophagy-related 5 (yeast) 11793 0.70 0.73 0.66 1.05 -0.23 ns Mtif2 mitochondrial translational initiation factor 2 76784 1.16 1.29 1.19 0.97 -0.36 ns Psap prosaposin 19156 8.07 7.25 8.37 0.96 0.02 ns Ube2g1 ubiquitin-conjugating enzyme E2G 1 (UBC7 homolog, C. elegans) 67128 4.02 3.60 3.88 1.03 -0.22 ns Zkscan3 zinc finger with KRAB and SCAN domains 3 72739 0.88 0.86 0.92 0.96 0.22 ns Mrpl27 mitochondrial ribosomal protein L27 94064 1.88 1.59 2.05 0.91 -0.22 ns Dlg1 discs, large homolog 1 (Drosophila) 13383 4.74 4.06 3.63 1.30 0.52 ns Canx calnexin 12330 8.75 8.46 8.92 0.98 -0.63 ns Psma1 proteasome (prosome, macropain) subunit, alpha type 1 26440 3.18 3.02 4.04 0.78 -0.67 ns Sar1a SAR1 gene homolog A (S. cerevisiae) 20224 2.69 2.17 1.88 1.43 0.88 * Gps1 G protein pathway suppressor 1 209318 3.26 2.83 3.10 1.05 0.47 ns Ctbp1 C-terminal binding protein 1 13016 3.99 4.83 5.02 0.79 -0.69 ns Huwe1 HECT, UBA and WWE domain containing 1 59026 2.05 2.28 3.13 0.65 -0.18 ns Cdv3 carnitine deficiency-associated gene expressed in ventricle 3 321022 4.01 3.89 3.12 1.28 0.84 * Copa coatomer protein complex subunit alpha 12847 3.95 3.57 3.27 1.20 0.80 ns Anapc2 anaphase promoting complex subunit 2 99152 2.20 2.00 1.61 1.36 0.77 ns Cox18 COX18 cytochrome c oxidase assembly homolog (S. cerevisiae) 231430 0.76 0.82 1.07 0.71 -0.82 * Arfgef1 ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A- 211673 6.19 5.53 4.52 1.36 0.15 ns inhibited) Zranb1 zinc finger, RAN-binding domain containing 1 360216 0.62 0.59 0.66 0.94 -0.28 ns Ddx24 DEAD (Asp-Glu-Ala-Asp) box polypeptide 24 27225 1.06 0.89 0.98 1.07 0.48 ns Tmem129 transmembrane protein 129 68366 0.38 0.53 0.61 0.61 -0.94 ** Rps27 ribosomal protein S27 57294 21.87 20.97 15.03 1.45 0.71 ns Sap30l SAP30-like 50724 1.13 1.20 1.77 0.64 -0.54 ns Mad2l1bp MAD2L1 binding protein 66591 0.76 0.75 0.52 1.46 0.92 ** Vta1 Vps20-associated 1 homolog (S. cerevisiae) 66201 1.72 1.50 1.69 1.01 -0.30 ns Eif5 eukaryotic translation initiation factor 5 217869 7.61 7.15 7.25 1.04 0.19 ns Rrn3 RRN3 RNA polymerase I transcription factor homolog (yeast) 106298 0.69 0.72 0.94 0.73 -0.92 * Apoa1bp apolipoprotein A-I binding protein 246703 3.97 4.27 3.45 1.14 0.40 ns Pdpk1 3-phosphoinositide dependent protein kinase-1 18607 2.48 2.14 1.53 1.62 0.92 ** 5730453I16Rik RIKEN cDNA 5730453I16 gene 269061 2.48 2.62 2.08 1.19 0.78 ns Bat5 HLA-B associated transcript 5 193742 1.01 0.75 0.54 1.86 0.92 ** Rab7 RAB7, member RAS oncogene family 19349 4.25 4.78 4.91 0.86 -0.46 ns Ddb1 damage specific DNA binding protein 1 13194 5.39 5.93 4.75 1.13 0.72 ns Txndc12 thioredoxin domain containing 12 (endoplasmic reticulum) 66073 1.53 1.59 1.93 0.79 -0.41 ns Psmc5 protease (prosome, macropain) 26S subunit, ATPase 5 19184 2.80 2.42 2.30 1.21 0.70 ns Tmem165 transmembrane protein 165 21982 3.13 3.10 3.66 0.85 -0.84 * Aup1 ancient ubiquitous protein 11993 1.06 1.07 1.00 1.05 -0.08 ns Hdac5 histone deacetylase 5 15184 0.62 0.56 0.95 0.65 -0.24 ns H2-Ke2 H2-K region expressed gene 2 14976 2.51 2.55 1.94 1.28 0.87 * Dscr3 Down syndrome critical region gene 3 13185 1.27 1.12 1.46 0.87 -0.37 ns Cic capicua homolog (Drosophila) 71722 0.70 0.82 1.00 0.69 -0.71 ns Riok3 RIO kinase 3 (yeast) 66878 1.35 1.33 1.45 0.93 0.29 ns Dctn5 dynactin 5 59288 0.91 0.86 1.13 0.80 -0.71 ns Rragc Ras-related GTP binding C 54170 1.56 1.52 1.48 1.05 -0.22 ns Tbl3 transducin (beta)-like 3 213773 0.62 0.70 0.51 1.21 0.72 ns Hp1bp3 heterochromatin protein 1, binding protein 3 15441 2.20 2.25 2.56 0.86 -0.29 ns BC031181 cDNA sequence BC031181 407819 1.49 1.70 1.66 0.89 -0.02 ns Polr2f polymerase (RNA) II (DNA directed) polypeptide F 69833 2.21 2.45 2.86 0.77 -0.48 ns Gbf1 golgi-specific brefeldin A-resistance factor 1 107338 0.89 0.90 0.76 1.17 0.18 ns Fryl furry homolog-like (Drosophila) 72313 1.28 1.07 1.19 1.07 -0.04 ns Atox1 ATX1 (antioxidant protein 1) homolog 1 (yeast) 11927 1.44 1.66 2.33 0.61 -0.62 ns 2510006D16Rik RIKEN cDNA 2510006D16 gene 76799 1.55 1.57 1.58 0.97 0.25 ns Zc3h11a zinc finger CCCH type containing 11A 70579 6.72 6.04 6.02 1.11 0.83 * Ube2r2 ubiquitin-conjugating enzyme E2R 2 67615 1.62 1.50 1.57 1.03 0.02 ns Itch itchy, E3 ubiquitin protein ligase 16396 1.93 1.89 2.32 0.83 -0.39 ns Ncl nucleolin 17975 9.80 11.07 7.21 1.35 0.63 ns Aldh3a2 aldehyde dehydrogenase family 3, subfamily A2 11671 0.41 0.36 0.47 0.87 -0.26 ns Actg1 actin, gamma, cytoplasmic 1 11465 25.73 24.15 21.65 1.18 0.72 ns LOC672381 672381 21.93 20.28 18.54 1.18 0.96 ** LOC675440 675440 21.93 20.28 18.54 1.18 0.96 ** Sumo2 170930 21.93 20.28 18.54 1.18 0.96 ** Vps35 vacuolar protein sorting 35 65114 6.87 6.05 6.64 1.03 0.45 ns Cct8 chaperonin subunit 8 (theta) 12469 4.12 3.97 4.91 0.84 -0.77 ns Ganab alpha glucosidase 2 alpha neutral subunit 14376 1.97 2.24 2.10 0.93 -0.67 ns Ublcp1 ubiquitin-like domain containing CTD phosphatase 1 79560 1.00 1.11 1.19 0.84 -0.40 ns Rnf34 ring finger protein 34 80751 0.79 0.87 0.72 1.10 0.01 ns Rbck1 RanBP-type and C3HC4-type zinc finger containing 1 24105 1.11 1.10 1.24 0.90 -0.50 ns Pnpo pyridoxine 5'-phosphate oxidase 103711 0.39 0.40 0.41 0.93 -0.44 ns Dazap2 DAZ associated protein 2 23994 7.50 7.47 8.84 0.84 -0.76 ns Wbp11 WW domain binding protein 11 60321 1.67 1.73 2.04 0.81 -0.85 * Slc16a1 solute carrier family 16 (monocarboxylic acid transporters), member 1 20501 6.17 6.01 4.84 1.27 0.26 ns Cx3cl1 chemokine (C-X3-C motif) ligand 1 20312 0.57 0.52 0.63 0.91 -0.58 ns Plat plasminogen activator, tissue 18791 0.08 0.15 0.52 0.16 -0.89 * Uhrf1 ubiquitin-like, containing PHD and RING finger domains, 1 18140 5.40 5.35 4.14 1.30 0.88 * Atp6v1b2 ATPase, H+ transporting, lysosomal V1 subunit B2 11966 1.52 1.47 1.43 1.06 0.39 ns Cct7 chaperonin subunit 7 (eta) 12468 5.26 6.19 6.55 0.80 -0.15 ns Anxa6 annexin A6 11749 1.37 1.29 1.51 0.91 0.30 ns Nptn neuroplastin 20320 4.51 3.53 3.51 1.28 0.83 * Scd2 stearoyl-Coenzyme A desaturase 2 20250 20.29 18.95 15.63 1.29 0.39 ns Atp6v1h ATPase, H+ transporting, lysosomal V1 subunit H 108664 1.30 1.41 1.28 1.01 -0.42 ns Lbr lamin B receptor 98386 3.08 3.89 3.39 0.91 0.30 ns Orc5l origin recognition complex, subunit 5-like (S.
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    Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4).
  • Patient-Based Cross-Platform Comparison of Oligonucleotide Microarray Expression Profiles

    Patient-Based Cross-Platform Comparison of Oligonucleotide Microarray Expression Profiles

    Laboratory Investigation (2005) 85, 1024–1039 & 2005 USCAP, Inc All rights reserved 0023-6837/05 $30.00 www.laboratoryinvestigation.org Patient-based cross-platform comparison of oligonucleotide microarray expression profiles Joerg Schlingemann1,*, Negusse Habtemichael2,*, Carina Ittrich3, Grischa Toedt1, Heidi Kramer1, Markus Hambek4, Rainald Knecht4, Peter Lichter1, Roland Stauber2 and Meinhard Hahn1 1Division of Molecular Genetics, Deutsches Krebsforschungszentrum, Heidelberg, Germany; 2Chemotherapeutisches Forschungsinstitut Georg-Speyer-Haus, Frankfurt am Main, Germany; 3Central Unit Biostatistics, Deutsches Krebsforschungszentrum, Heidelberg, Germany and 4Department of Otorhinolaryngology, Universita¨tsklinik, Johann-Wolfgang-Goethe-Universita¨t Frankfurt, Frankfurt, Germany The comparison of gene expression measurements obtained with different technical approaches is of substantial interest in order to clarify whether interplatform differences may conceal biologically significant information. To address this concern, we analyzed gene expression in a set of head and neck squamous cell carcinoma patients, using both spotted oligonucleotide microarrays made from a large collection of 70-mer probes and commercial arrays produced by in situ synthesis of sets of multiple 25-mer oligonucleotides per gene. Expression measurements were compared for 4425 genes represented on both platforms, which revealed strong correlations between the corresponding data sets. Of note, a global tendency towards smaller absolute ratios was observed when