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Bin 1 Bins 2 & 3 Bins 4 & 5 Bins 6 & 7 Bin 8 Bin 9 Bin 10 Accession Accession Accession Accession Accession Accession Accession Gene Name Gene Name Gene Name Gene Name Gene Name Gene Name Gene Name Number Number Number Number Number Number Number U70270 Mud-4 U70268 Mud-7 H31839 EST (Bak1) BCL2-antagonist/killer 1 U77829 Gas-5 growth arrest homolog AF025670 Caspase 6 (CASP6); MCH2 AA800243 EST (CIDE-A) Cell death inducing DNA fragmenta AA859938 EST (Bnip23l) BCL2/adenovirus E1B 19 kDa-inte AA818072 EST Bcl-2 associated death agonist AJ006971 DAP-like kinase U77829 Gas-5 growth arrest homolog U77933 Nedd2/Ich-1 M64733 Testosterone-repressed prostate message 2 AA891842 EST Death rec 6, (TNFRSF21) tumor necrosis fa U72995 MAP-kinase activating death domain AA891933 EST Smac protein, mitochondrial precursor, (seconU94340 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) U47315 R2 cerebellum DDRT-T-PCR AA875455 EST Wig1, p53-activated gene 608 U05989 Par-4 induced by effectors of apoptosis AA874794 EST (TNFRSF16) NGF receptor associated protein AA848545 EST Programmed cell death 10, TF-1 cell apoptosi AA874794 EST (TNFRSF16) NGF receptor associated protein U49930 Caspase 3, apoptosis related cysteine protease (IC U49930 Caspase 3, apoptosis related cysteine protease (IC U84410 Caspase 3, apoptosis related cysteine protease (IC AA891591 EST Programmed cell death 8 (apoptosis-inducing AA892388 EST Death-associated kinase 2 AF030358 Chemokine CX3C AA818894 EST (Pgsg) proteoglycan peptide core protein S79676 IL-1 Beta converting enzyme U14647 Interleukin 1beta converting enzyme AA874803 EST Chemokine (C-X-C motif) ligand 14 AA859645 EST (Atrn) gene for membrane attractin U70988 Chemokine (C-X-C) receptor 2 AA800602 EST Chemokine (C-X3-C motif) ligand 1 E01884 IL-1-beta U14647 Interleukin 1beta converting enzyme AA799520 EST Integral membrane protein 2B AA874803 EST Chemokine (C-X-C motif) ligand 14 AF030358 Chemokine CX3C S73424 Macrophage migration inhibitory factor AA818025 EST CD59 antigen M98820 Interleukin 1 beta (IL1-beta; IL1B) M63122 Tumor necrosis factor receptor D00403 Interleukin 1 alpha AF068860 Beta defensin-1 AA892179 EST Adapter prot CIKS(Connection to IKK SAPK/ AI009801 EST (MIF) macrophage migration inhibitory factor AI071435 EST Sacm21/RT1-A intergen regi haplotype RT1n/ M98820 Interleukin 1 beta (IL1-beta; IL1B) AJ012603 TNF-alpha converting enzyme (TACE) M58587 Interleukin 6 receptor U49062 CD24 antigen U48828 Retroviral-like ovarian specific transcript 30-1 D38455 Mast cell protease 6 M36151 MHC class II A-beta RT1.B-b-beta Z22812 IL-IR Type 2 AJ012603 TNF-alpha converting enzyme (TACE) U69272 Interleukin 15 U49062 CD24 antigen AA875148 EST Butyrate-induced transcript 1 (Hspc121-pend U67910 Mast cell protease 7 M15562 MHC class II RT1.u-D-alpha M26744 Interleukin 6 (interferon, beta 2) AJ012603 TNF-alpha converting enzyme (TACE) U68272 Interferon gamma receptor AI171462 EST CD-24 Z50144 Kynurenine/alpha-aminoadipate aminotransferase S79711 CD3, gamma chain X14254 MHC class II-associated invariant chain S77528 rNFIL-6=C/EBP-related transcription factor AI237535 EST LPS-induced TNF-alpha factor AA892259 EST Interferon concensus sequence binding prote AA818025 EST CD 59 antigen M29866 Complement component C3 U02506 Polymeric immunoglobulin receptor X14254 MHC class II-associated invariant chain X60769 Silencer factor B AA891690 EST Tumor necrosis factor (ligand) superfamily, m U17035 Interferon gamma-induced protein 10 (INP10; IP10M83143 Beta-galactoside-alpha 2,6-sialyltransferase M15402 Ig active kappa-chain U57063 Natural killer cell protease 7 M65149 CCAAT/enhancerbinding, protein (C/EBP) delta AA891690 EST Tumor necrosis factor (ligand) superfamily, m X61381 Interferon-induced protein AI103957 EST Tssc6 25 AA892240 EST MHC class I RT1.O type -149 processed pseuU94330 Osteoprotegerin AI045030 EST (Cebpd) CCAAT/enhancerbinding, protein (C/ AA800814 EST Tumor necrosis factor (ligand) superfamily, m M34253 Interferon regulatory factor 1 AI103957 EST Tssc6 AI231375 EST MHC class I RT1.Ac heavy chain precursor AF036548 RGC-32 (RGC-32) L32132 Lipopolysaccharide binding protein AA900380 EST Tumor necrosis factor receptor superfamily, mM34253 Interferon regulatory factor 1 AA875225 EST Guanine nucleotide binding prot, alpha inhibiti AF029240 MHC class Ib RT1.S3 (RT1.S3) AA859468 EST SHB (Src homology 2 domain containing) ada U50353 Defensin 3a AA799761 EST (Tnfrsf5) tumor necrosis factor receptor supe AA891944 EST Interferon-gamma induced GTPase AA893235 EST Go/G1 switch gene 2 AA892014 EST (Bat1a) HLA-B-associated transcript 1A AA875552 EST Myeloid leukemia factor 2 U22414 Macrophage inflammatory protein 1 alpha (Small inAA892960 EST Lipopolysaccharide specific response-7 protei AA799861 EST Interferon regulatory factor 7 X76453 Hras-revertant gene 107 D45240 MHC class II gene X86086 Annexin VI U45965 Macrophage inflammatory protein 2 (MIP2) AF055065 Signal regulatory protein alpha AA799861 EST Interferon regulatory factor 7 AA892132 EST D12 protein, uncharacterized hematopoietic s AA943555 EST (Lnk4,3 and 2) linker of T-cell receptor pathw U11681 Rapamycin and FKBP12 target-1 protein U06434 Macrophage inflammatory protein-1 beta AI639056 EST Interleukin 1 receptor accessory protein X52713 Myxovirus (influenza) resistance, homolog of murinAA686164 EST Dendritic cell protein AI176307 EST TCR gamma C4L=T-cell receptor gamma ch D86642 FK506-binding protein 12.6 X17053 Immediate-early serum-responsive JE U48592 Interleukin 1 receptor accessory protein L29281 Protein kinase, interferon-inducible double strande AI011179 EST Immunoglobulin binding protein, 1, alpha 4 ph C06598 Rapamycin-binding protein FKBp-13 AI231547 EST FK506 binding protein 4 (59 kDa) X17053 Immediate-early serum-responsive JE X69903 Interleukin 4 receptor (IL4R) Y07704 BEST-5 AA894045 EST NK receptor 1c7 AA818152 EST Peptidylprolyl isomerase A (cyclophilin A) AI103874 EST FK506 binding protein 3 (25kD) D11445 Rat gene for gro AF015719 IL-15 Y07704 BEST-5 AA799889 EST Natural killer tumor recognition sequence S78744 protein S-activated protein C cofactor AA684963 EST FK506 binding protein 2 (13 kDa) E13732 CC chemokine receptor U77777 Interleukin 18 U72741 Lectin, galactose binding, soluble 9 (Galectin-9) U16025 Class Ib RT1 D37951 c-myc intron binding protein 1 AI070108 EST FKBP-associated protein isoform FAP68 AF053312 Small inducible cytokine subfamily A20 AJ222813 Interleukin 18 AA799569 EST Signal transducer and activator of transcriptio U16025 Class Ib RT1 AA875090 EST Kappa b-RAS 2 (I-Kappa beta interacting RASAA800175 EST Protein (peptidyl-prolyl cis/trans isomerase AF075383 Cytokine inducible SH2-containing protein 3 Y12009 Chemokine co-receptor CKR5 AA925556 EST TNF intracellular domain-interacting protein X13044 MHC-associated invariant chain gamma X16481 Zinc(2+) binding protein D37880 Bruton agammaglobulinemia tyrosine kinase AA892308 EST C57BL/6J cytokine gene cluster U90610 CXC chemokine receptor AF057025 Toll-like receptor 4 X13044 MHC-associated invariant chain gamma AI638989 EST SH3-domain binding protein 3, strain C57BL/6L19180 Receptor-linked protein tyrosine phosphatase AI235631 EST Transmembr prot induced by tumor necrosis f U90610 CXC chemokine receptor AA893666 EST (Tlr7) toll-like receptor 7 AI639117 EST Histocompatibility 2, complement component AF026504 SPA-1 like protein p1294 AI011746 EST Transmembr prot induced by tumor necrosis f AJ223184 DORA protein L26267 NF-kappa-B transcription factor p105 subunit (NFKAI170268 EST b2 microglobulin, prostaglandin F2a AA875001 EST Tripartite motif protein 8 J05122 Benzodiazepine receptor (peripheral) AA945737 EST Chemokine receptor LCR1 AI639149 EST HIC protein isoform P 32 M30691 Ly6-B antigen D29646 CD38 antigen (ADP-ribosyl cyclase / cyclic ADP-ribAA892854 EST Small inducible cytokine submfamily (Cys-X-CX52477 Complement component 3 AF087943 CD14 AA819187 EST CD38 mRNA for ADP-ribosyl cyclase X13016 MRC OX-45 surface antigen U42719 Complement component 4 AA875126 EST B6-derived CD11 +ve dendritic cells D49955 Bone marrow stromal cell antigen 1 AF037067 OX40 ligand AA875126 EST B6-derived CD11 +ve dendritic cells AF087944 Monocyte differentiation antigen CD14 X53517 CD37 antigen AI231213 EST (Kai1) kangai 1 A30543 CD44 surface protein from patent WO9117248 M15768 CD4 antigen (p55) AJ223184 DORA protein M18349 Leukocyte common antigen X04310 CD8 antigen, beta-chain X56596 MHC class II antigen RT1.B-1 beta-chain M10072 Leukocyte common antigen (LCA); CD45 antigen; M57276 Leukocyte antigen (Ox-44) X53054 RT1.D beta chain X76489 CD9, surface glycoprotein, platelet K03039 Thymocyte L-CA AI010293 EST HLA-B-associated transcript 3 X61654 Cd63 antigen D50558 Membrane glycoprotein (CD-86) 50 AA866404 EST (H2-Ke6) H2-K region expressed gene 6 X03015 CD8 antigen, alpha-chain D50558 Membrane glycoprotein (CD-86) X63594 RL/IF-1 U39546 Surface protein MCA-32 M92059 Adipsin X63594 RL/IF-1 AA891475 EST Paired immunoglobulin-like receptor alpha, im X14323 IgG receptor FcRn large subunit p51 AB015433 Antigen identified by monoclonal antibodies 4F2 J05495 Gal/GalNAc-specific lectin X14323 IgG receptor FcRn large subunit p51 X82445 C15 AA894312 EST Recombining binding protein suppressor of haAI180013 EST Fc receptor, IgG, alpha chain transporter L35271 Acute myeloid leukemia 1 AI639338 EST Src-like adaptor protein U56863 Ly-49.9 antigen AI176170 EST FK506 binding protein 1a (12 kDa) AI171966 EST RT1.Mb, histocompatibility 2, class II, locus M AF065438 Mama AA892680 EST CYP10L (Cyp10l), sim to peptidylprolyl
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    Table 2. Significant

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    Contig Protein Description Symbol Anterior Posterior Ratio

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  • Supporting Information

    Supporting Information

    Supporting Information Figure S1. The functionality of the tagged Arp6 and Swr1 was confirmed by monitoring cell growth and sensitivity to hydeoxyurea (HU). Five-fold serial dilutions of each strain were plated on YPD with or without 50 mM HU and incubated at 30°C or 37°C for 3 days. Figure S2. Localization of Arp6 and Swr1 on chromosome 3. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position of Tel 3L, Tel 3R, CEN3, and the RP gene are shown under the panels. Figure S3. Localization of Arp6 and Swr1 on chromosome 4. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) in the whole chromosome region are compared. The position of Tel 4L, Tel 4R, CEN4, SWR1, and RP genes are shown under the panels. Figure S4. Localization of Arp6 and Swr1 on the region including the SWR1 gene of chromosome 4. The binding of Arp6- FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position and orientation of the SWR1 gene is shown. Figure S5. Localization of Arp6 and Swr1 on chromosome 5. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position of Tel 5L, Tel 5R, CEN5, and the RP genes are shown under the panels. Figure S6. Preferential localization of Arp6 and Swr1 in the 5′ end of genes. Vertical bars represent the binding ratio of proteins in each locus.
  • Table S2. Enriched GO Categories in Biological Process for the Shared Degs

    Table S2. Enriched GO Categories in Biological Process for the Shared Degs

    Table S2. Enriched GO categories in biological process for the shared DEGs photosynthesis (GO ID:15979) Fold Change ProbeID AGI Col-0(R) pifQ(D) Name Description /Col-0(D) /Col-0(D) A_84_P19035 AT1G30380 17.07 4.9 PSAK; PSAK (PHOTOSYSTEM I SUBUNIT K) A_84_P21372 AT4G12800 8.55 3.57 PSAL; PSAL (photosystem I subunit L) PSBP-1; PSBP-1 (OXYGEN-EVOLVING A_84_P20343 AT1G06680 12.27 3.85 PSII-P; ENHANCER PROTEIN 2); poly(U) binding OEE2; LHCB6; LHCB6 (LIGHT HARVESTING COMPLEX A_84_P14174 AT1G15820 23.9 6.16 CP24; PSII); chlorophyll binding A_84_P11525 AT1G79040 16.02 4.42 PSBR; PSBR (photosystem II subunit R) FAD5; ADS3; FAD5 (FATTY ACID DESATURASE 5); A_84_P19290 AT3G15850 4.02 2.27 FADB; oxidoreductase JB67; GAPA (GLYCERALDEHYDE 3- GAPA; PHOSPHATE DEHYDROGENASE A A_84_P19306 AT3G26650 4.6 3.43 GAPA-1; SUBUNIT); glyceraldehyde-3-phosphate dehydrogenase A_84_P193234 AT2G06520 14.01 3.89 PSBX; PSBX (photosystem II subunit X) LHB1B1; LHB1B1 (Photosystem II light harvesting A_84_P160283 AT2G34430 89.44 32.95 LHCB1.4; complex gene 1.4); chlorophyll binding PSAN (photosystem I reaction center subunit A_84_P10324 AT5G64040 26.14 7.12 PSAN; PSI-N); calmodulin binding LHB1B2; LHB1B2 (Photosystem II light harvesting A_84_P207958 AT2G34420 41.71 12.26 LHCB1.5; complex gene 1.5); chlorophyll binding LHCA2 (Photosystem I light harvesting A_84_P19428 AT3G61470 10.91 5.36 LHCA2; complex gene 2); chlorophyll binding A_84_P22465 AT1G31330 32.37 6.58 PSAF; PSAF (photosystem I subunit F) chlorophyll A-B binding protein CP29 A_84_P190244 AT5G01530 16.45 5.27 LHCB4
  • A Comprehensive Analysis of the Expression of Crystallins in Mouse Retina Jinghua Xi Washington University School of Medicine in St

    A Comprehensive Analysis of the Expression of Crystallins in Mouse Retina Jinghua Xi Washington University School of Medicine in St

    Washington University School of Medicine Digital Commons@Becker Open Access Publications 2003 A comprehensive analysis of the expression of crystallins in mouse retina Jinghua Xi Washington University School of Medicine in St. Louis Rafal Farjo University of Michigan - Ann Arbor Shigeo Yoshida University of Michigan - Ann Arbor Timothy S. Kern Case Western Reserve University Anand Swaroop University of Michigan - Ann Arbor See next page for additional authors Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Recommended Citation Xi, Jinghua; Farjo, Rafal; Yoshida, Shigeo; Kern, Timothy S.; Swaroop, Anand; and Andley, Usha P., ,"A comprehensive analysis of the expression of crystallins in mouse retina." Molecular Vision.9,. 410-419. (2003). https://digitalcommons.wustl.edu/open_access_pubs/1801 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. Authors Jinghua Xi, Rafal Farjo, Shigeo Yoshida, Timothy S. Kern, Anand Swaroop, and Usha P. Andley This open access publication is available at Digital Commons@Becker: https://digitalcommons.wustl.edu/open_access_pubs/1801 Molecular Vision 2003; 9:410-9 <http://www.molvis.org/molvis/v9/a53> © 2003 Molecular Vision Received 28 May 2003 | Accepted 19 August 2003 | Published 28 August 2003 A comprehensive analysis of the expression of crystallins in mouse retina Jinghua Xi,1 Rafal Farjo,3 Shigeo Yoshida,3 Timothy S. Kern,5 Anand Swaroop,3,4 Usha P. Andley1,2 Departments of 1Ophthalmology and Visual Sciences and 2Biochemistry and Molecular Biophysics, Washington University School of Medicine, St.