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Microarray analysis of V. cholerae genes differentially expressed in rabbit ileal loop fluid and mucus

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Vibrio cholerae

PROVIDER: GSE24408 | GEO | 2010/09/29

SECONDARY ACCESSION(S): PRJNA132959

REPOSITORIES: GEO

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Microarray analysis of V. cholerae genes differentially expressed in rabbit ileal loop fluid and mucus

Project description:This SuperSeries is composed of the following subset Series: GSE6217: Microarray analysis of V. cholerae genes differentially expressed in 12 h rabbit ileal loop fluid GSE24405: Microarray analysis of V. cholerae genes differentially expressed in 8 h rabbit ileal loop mucus GSE24406: Microarray analysis of V. cholerae genes differentially expressed in 12 h rabbit ileal loop mucus GSE24407: Microarray analysis of V. cholerae genes differentially expressed in 8h rabbit ileal loop fluid Refer to individual Series

2010-09-28 | E-GEOD-24408 | biostudies-arrayexpress

Microarray analysis of V. cholerae genes differentially expressed in 12 h rabbit ileal loop mucus

Project description:The mucus and cell-associated bacteria were isolated as a single fraction from ileal loops twelve hours post inoculation by scraping the epithelial surface of the intestine with a disposable plastic cell scraper after the loops had been cut open and gently rinsed in PBS buffer to wash away remaining luminal fluid. The mucus gel/cell associated fraction was suspended in Trizol and frozen on dry ice. Total RNA, which includes RNA from the infecting bacteria and from the host (see below), was isolated from the thawed Trizol suspension, treated with DNaseI (Applied Biosystems, Austin, TX) and cleaned by using the RNeasy kit (Qiagen, Valencia, CA).

2010-09-29 | GSE24406 | GEO

Microarray analysis of V. cholerae genes differentially expressed in 8 h rabbit ileal loop mucus

Project description:The mucus and cell-associated bacteria were isolated as a single fraction from ileal loops eight hours post inoculation by scraping the epithelial surface of the intestine with a disposable plastic cell scraper after the loops had been cut open and gently rinsed in PBS buffer to wash away remaining luminal fluid. The mucus gel/cell associated fraction was suspended in Trizol and frozen on dry ice. Total RNA, which includes RNA from the infecting bacteria and from the host (see below), was isolated from the thawed Trizol suspension, treated with DNaseI (Applied Biosystems, Austin, TX) and cleaned by using the RNeasy kit (Qiagen, Valencia, CA).

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Microarray analysis of V. cholerae genes differentially expressed in 8 h rabbit ileal loop mucus

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Microarray analysis of V. cholerae genes differentially expressed in 8h rabbit ileal loop fluid.

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Microarray analysis of V. cholerae genes differentially expressed in 8h rabbit ileal loop fluid.

Project description:Transcriptional analysis of wild-type V. cholerae isolated from the rabbit ileal loop was performed by quickly pelleting bacteria from the fluid accumulated in the ileal loops after 8 h of infection. The bacteria were then resuspended in Trizol reagent and frozen on dry ice. The wild-type bacteria from three independent experiments in three different rabbits were analyzed. RNA was isolated from the Trizol agent, treated with DNaseI (Ambion, Austin, Texas, United States), and cleaned by using the RNeasy kit (Qiagen, Valencia, California, United States). Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.

2010-09-28 | E-GEOD-24407 | biostudies-arrayexpress

Microarray analysis of V. cholerae genes differentially expressed in 12 h rabbit ileal loop fluid

Project description:Transcriptional analysis of wild-type V. cholerae isolated from the rabbit ileal loop was performed by quickly pelleting bacteria from the fluid accumulated in the ileal loops after 12 h of infection. The bacteria were then resuspended in Trizol reagent and frozen on dry ice. The wild-type bacteria from two independent experiments in two different rabbits were analyzed. RNA was isolated from the Trizol agent, treated with DNaseI (Ambion, Austin, Texas, United States), and cleaned by using the RNeasy kit (Qiagen, Valencia, California, United States). Labeling of cDNA and microarray hybridizations were performed as described [Yiliz et al. 2001, Mol. Micro. 53: 497-515]. Microarrays were scanned with a GenePix 400A instrument (Axon Instruments), using the GENEPIX 5.0 software. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2006-11-03 | GSE6217 | GEO

Transcription profiling of Vibro cholerae from rabbit ileal loop fluid 12 h post infection to identify differentially expressed genes

Project description:Transcriptional analysis of wild-type V. cholerae isolated from the rabbit ileal loop was performed by quickly pelleting bacteria from the fluid accumulated in the ileal loops after 12 h of infection. The bacteria were then resuspended in Trizol reagent and frozen on dry ice. The wild-type bacteria from two independent experiments in two different rabbits were analyzed. RNA was isolated from the Trizol agent, treated with DNaseI (Ambion, Austin, Texas, United States), and cleaned by using the RNeasy kit (Qiagen, Valencia, California, United States). Labeling of cDNA and microarray hybridizations were performed as described [Yiliz et al. 2001, Mol. Micro. 53: 497-515]. Microarrays were scanned with a GenePix 400A instrument (Axon Instruments), using the GENEPIX 5.0 software.

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Adaptive thresholds to detect differentially expressed genes in microarray data.

Project description:To detect changes in gene expression data from microarrays, a fixed threshold for fold difference is used widely. However, it is not always guaranteed that a threshold value which is appropriate for highly expressed genes is suitable for lowly expressed genes. In this study, aiming at detecting truly differentially expressed genes from a wide expression range, we proposed an adaptive threshold method (AT). The adaptive thresholds, which have different values for different expression levels, are calculated based on two measurements under the same condition. The sensitivity, specificity and false discovery rate (FDR) of AT were investigated by simulations. The sensitivity and specificity under various noise conditions were greater than 89.7% and 99.32%, respectively. The FDR was smaller than 0.27. These results demonstrated the reliability of the method.

| S-EPMC3163930 | biostudies-literature

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