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Gene expression profiles of various tissues under different physiological conditions

ABSTRACT: Rice is one of important crop and, the genome has been already completely sequenced. Moreover we collected more than 30K rice FL-cDNA clones as transcriptome resources. However, the cDNA collection did not reveal the transcription activity and specificity of expression. So, we designed 60-mer oligo array based on the array system of Agilent Technologies (GPL477) as custom array. For validation of the array, we tested the reproducibility of labeling and hybridization. After this validation, 22K rice oligo array was supplied from Agilent Technologies (GPL892). 1: reproducibility of labeling: mRNA of shoot sample was amplified and labeled more than 10 times with Cy3 and Cy5, and both Cy3- and Cy5-labeled cRNA was hybridized on a slide (self-hybridization), and validate the reproducibility of labeling. In addition, we also amplified and labeled mRNA of other samples with Cy3 and Cy5, and made a self-hybridization. The intensity data of these array was also indicated transcription activity of genes in these samples. Keywords: variety among tissues

ORGANISM(S): Oryza sativa Oryza sativa Japonica Group

PROVIDER: GSE7530 | GEO | 2008/04/01

SECONDARY ACCESSION(S): PRJNA99401

REPOSITORIES: GEO

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Gene expression profiles of various tissues under different physiological conditions

Project description:Rice is one of important crop and, the genome has been already completely sequenced. Moreover we collected more than 30K rice FL-cDNA clones as transcriptome resources. However, the cDNA collection did not reveal the transcription activity and specificity of expression. So, we designed 60-mer oligo array based on the array system of Agilent Technologies (GPL477) as custom array. For validation of the array, we tested the reproducibility of labeling and hybridization. After this validation, 22K rice oligo array was supplied from Agilent Technologies (GPL892). 1: reproducibility of labeling: mRNA of shoot sample was amplified and labeled more than 10 times with Cy3 and Cy5, and both Cy3- and Cy5-labeled cRNA was hybridized on a slide (self-hybridization), and validate the reproducibility of labeling. In addition, we also amplified and labeled mRNA of other samples with Cy3 and Cy5, and made a self-hybridization. The intensity data of these array was also indicated transcription activity of genes in these samples. Keywords: variety among tissues organisms: Oryza sativa ssp. japonica (Nipponbare) tissue: shoot, root, germinated seed, panicle, callus derived from more than 100 plants treatement1: cold stress (10 degreeC) time course1: 24, 48, 72 hours tissue1: shoot treatment2: drought stress (25% polyethylene glycol 6000) time course2: 1, 9, 24 hours tissue: shoot treatment3: flood and lay-down stress time course3: 1, 6, 24, 48 hours tissue3: shoot treatment4: flood stress time course4: 1, 24, 48, 72 hours tissue4: shoot treatment5: osmotic stress (260mM mannitol) for 24 hours tissue5: shoot treatment6: 150mM NaCl for 24 hours tissue6: shoot hybridization : two dye method hybridization: self-hybridization replication: Hybridization of shoot replicated 11 times, and germinated seed was twice. Other samples did not replicated. array: 1 array per 1 experiment (total 39 arrays)

2008-04-01 | E-GEOD-7530 | biostudies-arrayexpress

Cardiac endothelial in vivo responses to LPS

Project description:Transcriptional responses of cardiac endothelial cells isolated from Tie-2 GFP mice 4 h and 24 h after intraperitoneal LPS injection. Operon V1 long oligo set. Hybridization using Cy3 and Cy5 labeled amplified RNA. Keywords: parallel sample

2004-02-26 | GSE1042 | GEO

Differentially expressed genes from different developmantal stages in rice

2008-04-01 | GSE7531 | GEO

Differentially expressed genes under different stress conditions in rice

2008-04-01 | GSE7532 | GEO

DNA methylation profiling of ductal carcinoma in situ (DCIS)

Project description:Methylated genomic fragments from tumor DNA and matching normal control were enriched with the methylated-CpG island recovery assay (MIRA); amplified, labeled and hybridized on Agilent CpG island tiling oligo arrays. MIRA enriched samples from tumor were labeled with Cy5 while MIRA enriched DNA samples from normal tissue were labeled with Cy3. Keywords: Cancer

2009-02-18 | GSE14865 | GEO

Methylation profiling of lung squamous cell carcinomas vs surrounding normal tissue

Project description:Methylated genomic fragments from tumor and matching normal DNA were enriched with the methylated-CpG island recovery assay (MIRA); amplified, labeled and hybridized on Agilent CpG island tiling oligo arrays. Samples from tumor were labeled with Cy5 while the matching normal were labeled with Cy3 so that methylation differences can be detected. Keywords: Cancer

2007-11-17 | GSE9622 | GEO

Contribution of unique genes by individual cell lines to Universal Mouse Reference RNA

Project description:RNA from 11 individual mouse cell lines were reverse-transcribed to cDNA, labeled with Cy5 and cohybridized with Cy3-labeled UMRR onto 7,500-spot mouse oligo microarrays (UNC). The data was analyzed using GeneTraffic software. 300-1000 spots out of 8,000 were flagged on each microarray and excluded from further analysis. Spots with hybridization signals in Cy5 channel higher than 1000 and with Cy5/Cy3 ratio greater than 2 were collected and the number of spots with these characteristics on only one microarray was determined. A reference experiment design type is where all samples are compared to a common reference. Keywords: reference_design

2006-01-05 | GSE3974 | GEO

Novel N-terminal Glucocorticoid Receptor Isoforms with Unique Transcriptional Target Genes

Project description:Gene expression analysis was conducted using Agilent Human1Av2 arrays (Agilent Technologies, Palo Alto, CA). Two separate biological replicates of cytoplasmic RNA samples were harvested and purified from each of the U-2 OS cell lines stably expressing hGRalpha, -A, -B, -C3, or D3 treated with 100 nM DEX or vehicle for 6 hours using RNeasy Midi kits (Invitrogen). These RNA samples were amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 0.5 ng of total RNA, two cRNAs, one labeled with Cy3 and one labeled with Cy5 were produced for each sample according to the manufacturer’s protocol. Consequently, four separate chips were used for each of the isoforms at each treatment condition, yielding a total of 40 chips: 5 isoforms X 2 treatments (vehicle vs. hormone) X 2 biological replicates X 2 labeling dyes. For each two-color comparison, 750 ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol. Slides were washed as indicated in this protocol and then scanned with an Agilent Scanner. Data were obtained using the Agilent Feature Extraction software (v7.1), using defaults for all parameters. Keywords: other

2005-06-20 | GSE2428 | GEO

expression of SATs

Project description:Expression of the sense-antisense transcripts (SATs). Methods: The sequences of 60mer DNA specific to the sense and antisense genes were chosen by K.K. DNAFORM (Japan), and Agilent Technologies manufactured custom oligo DNA microarray chips by using this information. RNA was labeled and hybridized using Fluorescent Direct Label Kits (oligo dT-primed labeling) (Agilent Technologies), according to the manufacturer's protocols. For labeling with random nanomers, we used the CyScribe First-Strand cDNA Labeling Kit (Amersham). The RNA samples used for microarray experiments were from mouse ES cells, SL10 cells (fibroblast cell line), brain, heart, and testis. The total RNA of brain, heart, and testis for array experiments was purchased from Ambion. The total RNA of ES and fibroblast cells was isolated using Trizol reagent (Invitrogen). The same total RNA samples were reciprocally labeled with Cy3 or Cy5, hybridized to the oligo DNA on the chip, and dye-normalized, and processed signals were obtained using Feature Extraction software (Agilent Technologies). Keywords: parallel sample

2005-03-31 | GSE2185 | GEO

Array-CGH of human hepatocellular carcinoma

Project description:Comparison of normal versus tumor DNA (hepatocellular carcinoma). Whole-genome screening of DNA-copy number changes by array-based or matrix comparative genomic hybridization (aCGH). Tumor DNA labeled in Cy3 and pooled DNA of lymphocytes from healthy donors labeled in Cy5. Keywords: Genetic modification

2007-10-15 | GSE8351 | GEO

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