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Expression data of colon cancer by conventional microarray and by suppressive subtractive hybridization coupled to microarray

ABSTRACT: Transcriptional profiling of colonic tumors compared to paired adjacent non-tumoral colonic tissue by two strategies. The first strategy is a conventional microarray assay, while the second strategy involves a previous Suppression Subtractive Hybridization (SSH) followed by a conventional microarray assay. We applied subtractive hybridization followed by microarray analysis to identify tumor-specific low-abundance transcripts. The goal was to determine differences in gene expression profile in tumor samples by both strategies.

ORGANISM(S): Homo sapiens

PROVIDER: GSE38939 | GEO | 2012/06/27

SECONDARY ACCESSION(S): PRJNA169537

REPOSITORIES: GEO

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Expression data of colon cancer by conventional microarray and by suppressive subtractive hybridization coupled to microarray

Project description:Transcriptional profiling of colonic tumors compared to paired adjacent non-tumoral colonic tissue by two strategies. The first strategy is a conventional microarray assay, while the second strategy involves a previous Suppression Subtractive Hybridization (SSH) followed by a conventional microarray assay. We applied subtractive hybridization followed by microarray analysis to identify tumor-specific low-abundance transcripts. The goal was to determine differences in gene expression profile in tumor samples by both strategies. Two-condition experiment: tumoral vs. adjacent non-tumoral tissues. Biological replicates: 10 tumoral replicates, 10 non-tumoral replicates. The same replicates were used for both strategies (conventional, SSH). Human Universal Reference RNA (Clontech) was used as the reference.

2012-06-26 | E-GEOD-38939 | biostudies-arrayexpress

Expression data of gastric cancer by conventional microarray and by suppressive subtractive hybridization coupled to microarray

2012-06-27 | GSE38932 | GEO

Expression data of gastric cancer by conventional microarray and by suppressive subtractive hybridization coupled to microarray

Project description:Transcriptional profiling of gastric tumors compared to paired adjacent non-tumoral gastric tissue by two strategies. The first strategy is a conventional microarray assay, while the second strategy involves a previous Suppression Subtractive Hybridization (SSH) followed by a conventional microarray assay. We applied subtractive hybridization followed by microarray analysis to identify tumor-specific low-abundance transcripts. The goal was to determine differences in gene expression profile in tumor samples by both strategies. Two-condition experiment: tumoral vs. adjacent non-tumoral tissues. Biological replicates: 12 tumoral replicates, 12 non-tumoral replicates. The same replicates were used for both strategies (conventional, SSH). Human Universal Reference RNA (Clontech) was used as the reference.

2012-06-26 | E-GEOD-38932 | biostudies-arrayexpress

Human Tissues: pancreatic cancer vs. pancreatic non-tumoral tissues

Project description:Transcriptional profiling of pancreatic tumors comparing to adjacent non-tumoral pancreatic tissue by two strategies. The first strategy implies a traditional microarray assay, while the second involves a previous Suppression Subtractive Hybridization (SSH) and then the traditional microarray assay. Goal was to determine differences in gene expression profile in tumor samples by both strategies.

2012-07-31 | GSE39751 | GEO

Human Tissues: pancreatic cancer vs. pancreatic non-tumoral tissues

2012-07-30 | E-GEOD-39751 | biostudies-arrayexpress

Identification of salt stress regulated genes in tomato seedlings by SSH and microarray analysis

Project description:High salinity is one of the most serious threats to crop production. To 1 better understand the molecular basis of plant responses to salt stress, we combined suppression subtractive hybridization (SSH) and microarray approaches to identify the potential important or novel genes involved in salt tolerance. First, SSH libraries were constructed for two cultivated tomato (Solanum lycopersicum) genotypes: LA2711, a salt tolerant cultivar, and ZS-5, a salt sensitive cultivar, to compare salt treatment and non-treatment plants. Then a subset of clones from these SSH libraries were used to construct a tomato cDNA array and microarray analysis was carried out to verify the expression changes of this set of clones upon salt treatment at various time points compared to the corresponding non-treatment controls. A totalof 201 non-redundant genes differentially expressed upon 30 min of salt stress treatment either in LA2711 or ZS-5 were identified from microarray analysis, most of which were not previously associated with salt stress. The diversity of the putative functions of these genes indicated that salt stress resulted in a complex response in tomato plants. Keywords: gene expression, genotype, microarray, salt stress, SSH, tomato

2007-01-09 | GSE4961 | GEO

Gene expression data from advanced gastric and colon cancers: tumoral vs. matched non-tumoral tissues

Project description:This SuperSeries is composed of the following subset Series: GSE38932: Expression data of gastric cancer by conventional microarray and by suppressive subtractive hybridization coupled to microarray GSE38939: Expression data of colon cancer by conventional microarray and by suppressive subtractive hybridization coupled to microarray Refer to individual Series

2012-06-26 | E-GEOD-38940 | biostudies-arrayexpress

A genomic approach to bud mutation in sweet orange (Citrus sinensis L. Osbeck) fruit

Project description:Bud mutations arise often in citrus. The selection of mutants is one of the most important breeding methods in citrus. However, the molecular bases of bud mutation have rarely been studied. To identify the potential important or novel genes involved in bud mutation, different transcriptomic techniques combing suppression subtractive hybridization (SSH) and microarray were performed between a lycopene accumulated mutant, ‘Hong Anliu’ sweet orange (Citrus sinensis L. Osbeck), and its wild-type during fruit maturation. Microarray analysis revealed that differentially expressed clones are extensively coordinated with the initiation of lycopene accumulation. After sequencing of the differentially expressed clones, a total of 267 non-redundant transcripts were obtained, 182 (68.2%) of which share homology (E-value ≤ 1×10-10) with known gene products or known protein domains. A list of candidate genes which involved in cellular metabolic process, primary metabolic process, localization, macromolecular metabolic process was obtained. Out of these genes, 12 share homology with previously described signal transduction or transcription factors, suggesting complex regulatory control. These results demonstrate profound effect on gene expression of bud mutation in citrus fruits and provide new insights into the molecular basis of bud mutation. Keywords: bud mutation, candidate genes, Citrus, cNDA microarray, suppression subtractive hybridization (SSH)

2009-03-10 | GSE10729 | GEO

Expression Profiling to Identify Novel Desiccation Response Transcripts from Tortula ruralis gametophytes

Project description:In this study we have tried to utilize the unique aspects of the T. ruralis response to desiccation and rehydration to design a strategy to identify rehydrins that are of low abundance and perhaps completely novel to the desiccated or rehydration transcriptomes. We have constructed two Subtractive Suppression Hybridization (SSH) libraries (Diatchenko et al., 1996) that are designed to enrich for differentially expressed low-abundance transcripts contained within gametophytic cells either in the slow-dried state (mRNP sequestrated rehydrin transcripts) or cells that have been rapidly dried, rehydrated and sampled at 2h of hydration (rehydrin and recovery transcripts) when the translational change in gene expression is at its peak (Oliver 1991). To achieve this aim we constructed SSH libraries using PolyA RNA isolated from the polysomal (mRNP) fractions from the slow-dried and 2h rehydrated rapid dried gametophytes selected against PolyA RNA from hydrated control gametophytes as the source for driver cDNA. Collections of cDNA clones from each library were sequenced and used to generate a small T. ruralis SSH cDNA microarray for expression profiling of both total RNA extracts for transcript accumulation assessments and polysomal RNA extracts for transcript sequestration and recruitment assessments.

2009-01-31 | GSE13680 | GEO

Homo sapiens

Project description:Expression data of gastric cancer by conventional microarray and by suppressive subtractive hybridization coupled to microarray

| PRJNA169536 | ENA

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