oligo type of microarray  (Oligos Etc)

Journal: PLoS Genetics

Article Title: Identification and Functional Analysis of Light-Responsive Unique Genes and Gene Family Members in Rice

doi: 10.1371/journal.pgen.1000164

Figure Lengend Snippet: (A) The seven steps in the rice chlorophyll biosynthesis pathway, from magnesium chelatase to chlorophyll b, are shown and mutants of rice corresponding to each step are indicated. Red boxes indicate mutants which have been characterized in rice. CHLH, magnesium-chelatase subunit H family protein (1); CHLI, magnesium-chelatase subunit I family protein (1); CHLD, magnesium chelatase ATPase subunit D protein (1); CHLM, magnesium-protoporphyrin O-methyltransferase (2, and there were two gene family members); MPE, magnesium-protoporphyrin IX monomethyl ester cyclase (3); DVR, divinyl protochlorophyllide reductase (4, and there were five gene family members); POR, protochlorophyllide reductase (5, and there were four gene family members); CHLG, chlorophyll synthase (6, and there were two gene family members); and CAO, chlorophyll a oxygenase (7, and there were two gene family members). oschlh , chlorina-1 , and -9 are mutants in rice ChlH , ChlI , ChlD , respectively; xantha-f , g , and h are mutants in barley ChlH , ChlI , ChlD , respectively; cs/ch42 is mutant in Arabidopsis CHLI ; gun5 is mutant in Arabidopsis CHLH ; chlm is mutant in Arabidopsis CHLM ; albino-39 is mutant in rice ChlM ; Chl27 is mutant in Arabidopsis MPE ; xantha-i is mutant in Barley Mpe ; dvr is mutant in Arabidopsis DVR ; porb-1porc-1 is double mutant of Arabidopsis PORB and PORC ; ygl1 is mutant of rice ChlG ; cao is mutant of Arabidopsis CAO ; and oscao1 is mutant of rice Cao1 . (B) Normalized average expression levels in light and dark and fold changes in expression from dark to light based on results of the NSF45K light vs. dark microarray experiment are shown for genes involved in the 7 steps in the pathway and their gene family members. Unique genes or gene family members predominantly expressed in the light in each step are marked with asterisks. White boxes indicate gene expression levels in light. Black boxes indicate gene expression levels in dark. Gray boxes indicate the fold change ratios of light over dark. Red boxes indicate the gene expression patterns of the genes corresponding to those mutations in red boxes of A. 1a , Os03g20700 ; 1b , Os03g36540 ; 1c , Os03g59640 ; 2-1 , Os06g04150 ; 2-2 , Os02g35060 ; 3 , Os01g17170 ; 4-1 , Os03g22780 ; 4-2 , Os02g56690 ; 4-3 , Os08g17500 ; 4-4 , Os08g34280 ; 4-5 , Os09g25150 ; 5-1 , Os04g58200 ; 5-2 , Os10g35370 ; 6-1 , Os05g28200 ; 6-2 , Os03g09060 ; 7-1 , Os10g41780 ; and 7-2 , Os10g41760 . (C) RT-PCR results are shown; Ubq1 and Actin1 were used as controls . Numbers of PCR cycles are indicated. IL, leaves from IR24 plants harvested in the light; ID, leaves from IR24 plants harvested in the dark; TL, leaves of Taipei (TP) 309 plants harvested in the light; TD, leaves of TP309 plants harvested in the dark; NL, leaves of Nipponbare plants harvested in the light; ND, leaves of Nipponbare plants harvested in the dark; KL, leaves of Kitaake plants harvested in the light; and KD, leaves of Kitaake plants harvested in the dark. ChlH , Os03g20700 ; ChlI , Os03g36540 ; ChlD , Os03g59640 ; ChlM , Os06g04150 , Os02g35060 ; Mpe , Os01g17170 ; Dvr1 , Os03g22780 ; Dvr2 , Os02g56690 ; Dvr3 , Os08g17500 ; Dvr4 , Os08g34280 ; Dvr5 , Os09g25150 ; Por1 , Os04g58200 ; Por2 , Os10g35370 ; ChlG1 , Os05g28200 ; ChlG2 , Os03g09060 ; Cao1 , Os10g41780 ; and Cao2 , Os10g41760 .

Article Snippet: The Rice Multi-platform Search page ( http://www.ricearray.org/matrix.search.shtml ) is a tool that allows users the ability to search across four different rice oligo microarray platform types (Affymetrix, Agilent, BGI/Yale, and NSF45K) to determine which oligos from each platform represent to a common gene target.

Techniques: Mutagenesis, Expressing, Microarray, Reverse Transcription Polymerase Chain Reaction

Journal: PLoS Genetics

Article Title: Identification and Functional Analysis of Light-Responsive Unique Genes and Gene Family Members in Rice

doi: 10.1371/journal.pgen.1000164

Figure Lengend Snippet: (A) The flow chart of functional analysis using microarray and gene-indexed mutants. (B) Gene expression patterns of selected 37 candidate genes and summary of functional analyses using gene-indexed mutants of these genes. is adapted from a previous review article . Dotted lines in indicate the cut region of rice seedlings used for this array experiment. The NSF45K and BGI/Yale light vs. dark array datasets were used to refine the list of 37 candidate genes prior to functional validation. Unique genes (U), genes without gene family members, are distinguished from genes (GF) with gene family members. The gene among the gene family members predominantly expressed in the light was marked as P, distinguished from non predominant genes (NP). The consistency of a gene's expression pattern among the NSF45K and BGI/Yale light vs. dark array data was noted with a Yes or No or 45K; 45K indicating the unavailability of any other reference array data for comparison. The genes for which functional analyses was performed are marked Yes. Co-segregation of the observed phenotype and a T-DNA insertion is indicated by Yes, No or ND; ND indicates that co-segregation was not determined due to somaclonal variation or problems with primers. Yellow box indicates rice light vs. dark microarray data derived using NSF45K and BGI/Yale array. Red box indicates gene expression data in leaf, seedling shoot, and young leaf derived using the Affymetrix array.

Article Snippet: The Rice Multi-platform Search page ( http://www.ricearray.org/matrix.search.shtml ) is a tool that allows users the ability to search across four different rice oligo microarray platform types (Affymetrix, Agilent, BGI/Yale, and NSF45K) to determine which oligos from each platform represent to a common gene target.

Techniques: Functional Assay, Microarray, Expressing, Derivative Assay

Journal: PLoS Genetics

Article Title: Identification and Functional Analysis of Light-Responsive Unique Genes and Gene Family Members in Rice

doi: 10.1371/journal.pgen.1000164

Figure Lengend Snippet: Hierarchical clustering analysis was carried out for 72 genes related to the 10 mutants shown in ; cluster results are indicated on the far left side of this figure. In the left panel, the log 2 fold change values of the 10 datasets used to perform hierarchical clustering analysis are shown (for details of the 10 datasets and how they were analyzed see ). The middle panel indicates the average of all spot intensities for an oligo in the light (av_NSF45K_light intensity) and dark (av_NSF45K_dark intensity) from NSF 45K light vs. dark datasets as another indicator of gene expression levels. Oligo_id indicates the name of the oligos in NSF45K array; Putative function describes the annotation assigned to that gene; Pathway indicates the biochemical pathway and step in the pathway associated with the gene; Type indicates status of the gene in the rice genome: U, unique sequence; P, predominantly expressed gene family member in the light; and NP, not the predominantly expressed gene family member in the light; CC-GO_term, indicates GO terms within the cellular component category; Rice Mutant indicates the phenotype associated with a mutation in the gene; and Reference provides citations to published evidence for the phenotypes described in the previous column. More information regarding U1, U3, U4, U5, U10, U11, P2-1, P5-1, P9-1, and P13-1 is contained in . In the column labeled CC-GO_term: Ch indicates chloroplast; Cy, cytoplasm; ER, endoplasmic reticulum; Mi, mitochondrion; Me, membrane; N, nucleus; and P, peroxisome. Data used for clustering analysis and more detailed information regarding the 72 genes on which the analysis was performed are contained in .

Article Snippet: The Rice Multi-platform Search page ( http://www.ricearray.org/matrix.search.shtml ) is a tool that allows users the ability to search across four different rice oligo microarray platform types (Affymetrix, Agilent, BGI/Yale, and NSF45K) to determine which oligos from each platform represent to a common gene target.

Techniques: Expressing, Sequencing, Mutagenesis, Labeling

Journal: PLoS Genetics

Article Title: Identification and Functional Analysis of Light-Responsive Unique Genes and Gene Family Members in Rice

doi: 10.1371/journal.pgen.1000164

Figure Lengend Snippet: (A) Validation of microarray data corresponding to genes in this pathway using RT-PCR amplifications. Ubq1 and Actin1 were used as controls for RT-PCR . Numbers of PCR cycles are indicated. See legend for for explanation of column heading abbreviations. Dxs1 , Dxs2 , Dxs3: gene family members encoding 1-deoxy-D-xylulose-5-phosphatesynthase; Dxr : gene encoding 1-deoxy-D-xylulose 5-phosphate reductoisomerase (2 in B); Cmt : gene encoding 2-C-methyl-D-erythritol4-phosphate cytidylyl transferase (3 in B); Cmk : gene encoding 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (4 in B); Mcs : gene encoding 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (5 in B); Hds : gene encoding 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (6 in B); Hdr1 , Hdr2 : gene family members encoding 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (7 in B) and there were two gene family members; and Idi1 , Idi2 : gene family members encoding isopentenyl-diphosphate delta-isomerase (8 in B) and there were two gene family members. (B) Proposed pathway model for explaining altered expression patterns. The MEP pathway was generated using RiceCyc ( http://www.gramene.org/pathway/ ). Twelve candidate genes were assigned to 8 steps in the pathway. Blue colored letters and arrows indicate the suppression of gene expression in dxr mutant; black ones indicate not significantly changed gene expression patterns in dxr mutant; and red ones indicate significantly induced gene expression patterns in dxr mutant. Phenotypes in T-DNA insertional homozygous progenies in Mcs gene is displayed in . (C) RT-PCR analysis of twelve candidate genes in this pathway in the rice dxr mutant (homozygous siblings) and its wild-type segregants. Genes indicated in red were up-regulated in the dxr mutant. Genes indicated in blue were down-regulated in the dxr mutant. Expression of genes indicated in black was not significantly changed in the dxr mutant. WT1, wild-type segregant 1; WT2, wild-type segregant 2; Ho-1, dxr homozygote 1; Ho-2, dxr homozygote 2. Ubq1 were used as controls for RT-PCR. RT-PCR amplifications were carried out as described in .

Article Snippet: The Rice Multi-platform Search page ( http://www.ricearray.org/matrix.search.shtml ) is a tool that allows users the ability to search across four different rice oligo microarray platform types (Affymetrix, Agilent, BGI/Yale, and NSF45K) to determine which oligos from each platform represent to a common gene target.

Techniques: Microarray, Reverse Transcription Polymerase Chain Reaction, Expressing, Generated, Mutagenesis