databaseArrayExpressfile_versionsfilesTxt P RenouXavier BarletSandra PelletierMarie-Laure L Martin-MagnietteYves MarcospeciesArabidopsis Thalianasubmitter_keywordstranscription profiling by arrayfull_dataset_link Protocol - whole plant - Media : Murashige & Skoog + Vitamines Temperature : 25°C Light : 8h: Sample Processing - no treatment Hybridization - Clv1.12_a Cy5 / WS_A Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream. Labeling - labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN). Nucleic Acid Extraction - Clv1.12_b:1ng.data_protocolAssay Data Transformation - ID_REF = ID number<br>VALUE = Normalized log2 ratio median intensity of Ch1(Cy5)/Ch2(Cy3) (Ch2=reference) Feature Extraction - The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock. Image Adquisition - GenePix Pro 3.0, Cy3:pmt voltage 532nm,500V,laser power 35%, Cy5:635nm,pmt voltage 500V,laser power 30%sample_synonymsSchwachman-Diamond syndrome, Schwachmann-Diamond syndrome, IL1BC, CASP-1, tree (narrow), BOUND WATER, House Dust, Visible Light, microarray hybridization protocol, oxidane, InChIKey=XLYOFNOQVPJJNP-UHFFFAOYAF, HOH, SDS, KL receptor activity, Gsfsco1, exact), herb (narrow), congenital, concavities, SEC, SCO5, SCO1, Il1bc, Gsfsow3, Gsfsco5, 2310040B03Rik, treatment, Chip, ChIP, N, sec, complementary DNA, min, CHIP, W, IL-1BC, Cy5, lipomatosis of pancreas, ICE, gametophyte (narrow), AA409961, anatomical tube, frutex (narrow), sample, disease management, AW046544, P11, dihydridooxygen, Bs, Shwachman-Bodian syndrome, dihydrogen oxide, Natriumhydroxid, hydroxyde de sodium, Sl, compressed, p61-Yes, Radiation, Caspase-1 subunit p10, Alcohol, iCE, p10, Arts, Sodium hydroxide, p11, aqua, AI836084, Tr-kit, Light, Pflanzenkoerper, Isopropyl Alcohol, PBT, H2O, Housedust, LIGHT, bush (narrow), Stickstoff, liana (narrow), Rubbing Alcohol, fossae, seedling (narrow), dense, CLP11, KIT, Hydrogen Oxide, Isopropanol, SDCCAG7, PCR, Visible Radiations, tyrosine-protein kinase Kit, Visible Radiation, Industrial, Yes, HVEML, Industrial Arts, NaOH, unit per litre, colony (related), vitamines, P45, Shwachman-Diamond type metaphyseal dysplasia, hydrogen hydroxide, depressions, clonal colony (related), Shwachman syndrome, sodium hydrate, ANX2LG, ANX2L, 管道, acqua, polymerase chain reaction, squashed, prothalli (narrow), nitrogen, GP11, woody clump (narrow), frutices (narrow), duct, p45, labeling protocol, microarray, Dust, Wasser, 7N, vitaminum, prothallus (narrow), pancreatic insufficiency and bone marrow dysfunction, HSPABP2, vitamine, genet (broad), 酪氨酸蛋白激酶试剂盒, 2210017D18Rik, SCF receptor activity, p60c-yes, SCAR16, vitamina, shrub (narrow), agua, AL024248, House, sodium hydroxide, U/l, 原癌基因c-Kit, light, SCFR, 解剖管, Fdc, cyanine-5-deoxycytosine triphosphate, [H]O[H], NY-CO-7, fossa, Isopropyl, Selb, PCE-2, vitaminas, 4733401P19Rik, Cal1l, labeling, soude caustique, Visible, eau, concavity, RANDOM, Caspase-1 subunit p20, congenital lipomatosis of pancreas, vitamins, Ca[1], TR2, UBOX1, 2 Propanol, 0610033N24Rik, sporophyte (narrow), CAL12, proto-oncogene c-Kit, compact, 42C, vine (narrow), InChI=1/H2O/h1H2, CE-2, cDNA, CD258, buffer, SOW3., Shwachman-Diamond syndrome, CAL1L, Temperatures, KIT ligand receptor activity, caustic soda, HNaO, CES2A1, soda lye, cell surface groove, Random selection by shearing, Radiations, furrow, c-KIT, groove, waterbath, line delineating groove, HsT441, Photoradiation, SWDS, Chromatin Immunoprecipitation, Shwachman-Bodian-Diamond syndrome, c-Yes, IL-1 beta-converting enzyme, planta entera (Spanish, azote, Interleukin-1 beta-converting enzyme, CGI-97, CD117, prothallium (narrow), sample population, LTg, nitrogeno, Interleukin-1 beta convertase, ramet (broad), P61-YES, Rubbing, Photoradiations, C-Kit, suffrutex (narrow), Pancreatic insufficiency and bone marrow dysfunction, Ssm,, Aetznatron, c-yes, [OH2], 植物体全体 (Japanese, depression, suffrutices (narrow)description_synonymsbacteria, keywords, Pseudomonas solanacearum, Sfrs8, SH3D1B, Transcriptome, SH3P18, determination, Transcriptome Profile, increased resistance, Bacillus solanacearum, AUTSX5, Expression Profiles, DXS648, Gene Expression Profile, AW212079, Gene, eubacteria, Profiles, QM, whole transcriptome, Srsf8, 6330437E22Rik, Gene Expression, Bacteria <prokaryote>, Expression Signatures, Gene Expression Signatures, chemical analysis, resistance, bact-, prokaryotes, NOV, SWAP, Gene Expression Signature, DBA12, Expression Profile, EC45, Transcriptome Profiles, AI197402, RPL10, Eubacteria, Bacteria <prokaryotes>, not Bacteria Haeckel 1894, RPYL10, Profile, DXHXS648E, RPLY10, 1190005N23Rik, D0HXS648, SFRS8, Monera, Signatures, SWA, PRO2015., Burkholderia solanacearum, DXHXS648, QM16, high resistance to, L10, Expression Signature, prokaryote, Prokaryotae, 真细菌(eubacteria), Gene Expression Profiles, Transcriptomes, L15, dye, Procaryotae, assay, DXS648E, Signature, Prokaryotadata_synonymsScientific Bias, Bru, PLIP, Raw, Ecological Fallacy, Truncation, number, IMAGE, Systematic Bias, presence, Type 2A-interacting protein, ESA1, Intervention or Procedure, THOC4, Epidemiologic Biase, Ecological, Del(8)44H, HTATIP, S-adenosyl-L-methionine:phenol O-methyltransferase activity, ALY|REF, Fallacies, Svc, hYAK3-2, Ecological Biases, proportion, Pip92, interventionDescription, Ch1, Aggregation, Interventional, number of, study assay, SURGICAL AND MEDICAL PROCEDURES, Cy5, BEF, data processing, cPLA2, Statistical Biases, scientific observation, CH1, has or lacks parts of type, RED, dye, Ecological Bias, REF, Systematic, Epidemiologic Biases, TIP, ratio, Biase, DYRK5, measuring, Intervention Strategies, Fallacy, data, light amplification by the stimulated emission of radiation., Scientific, ZC2HC5, ALY, Epidemiologic, Truncation Biases, extra or missing physical or functional parts, Ecological Fallacies, HTATIP1, Procedure, feature_extraction, CSA2, light amplification by the stimulated emission of radiation, AI317238, mereological quality, Outcome Measurement Errors, any method, Putative MAPK-activating protein PM10, count in organism, Experimental, count, batch, Errors, median, background, Truncation Bias, TIP60, Intervention, Bias, Col4a-1, proportionality, Biases, rate, Outcome Measurement, REDK, introduction, Experimental Bias, data analysis, Outcome Measurement Error, Error, Aggregation Bias, cardinality, Statistical Bias, quotient, 数据, microarray, quantitative, PMT, Statistical, TIP41, presence or absence in organismname_synonymsGenetic Materials, Cistron, Gene, Materials, Genetic Material., Genetic, Material, Cistronsview_count126isClaimabletruesearch_count1search_domainspatentfamilies~0rfam~0merops~0complex-portal~0uniprot~0wormbaseparasite~0biomodels_parameters~0reactome~0emdb~0wgs_masters~0ebiweb_resources~0ipd-mhc~0genome_assembly~0taxonomy~1ebiweb_people~0enzymeportal_enzymes~0pdbe~0chebi~0patentproteins~0interpro7~0uniref~0chembl~0gpcrdb~0hgnc~0intact~0rhea~0imgt-hla~0patentnucleotides~0ensemblroot~0non-coding~0europepmc~0identifiers_registry~0pdbechem~0biosamples~0interpro~0biotools~0mesh~0coding~0sra~0efo~0project~0human_diseases~0embl~0treefam~0uniparc~0ols~0dgva~0intenz~0go~0tsa_masters~0ebiweb_corporate~0omim~0sbo~0lrg~0ipd-kir~0rnacentral~0orcid_data_claims~0metagenomics~0pfam~0citation_count0citation_count_scaled0.0reanalysis_count_scaled0.0view_count_scaled0.0025665704202759063download_count_scaled0.0additional_accessionGSE18757is_claimabletruenameStudies of two mutants for clavata genes (clavata-ralstonia)descriptionra08-02_clavata-ralstonia - clavata-ralstonia - Clavata1 (Clv1.12) and clavata2 (RPL10) mutants display an increased resistance to the bacteria Ralstonia solanacearum. Transcriptome analysis aims to understand resistance mechanisms. - 3 biological repets Keywords: wt vs mutant comparison 6 dye-swap - CATMA arraysdatespublication2009-10-30updated2014-05-02accessionE-GEOD-18757cross_referencesTAXONOMY3702