Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1045384 | ENA |
REPOSITORIES: ENA
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Project description:Understanding the bacterial community structure, and their functional analysis for active bioremediation process is essential to design better and cost effective strategies. Microarray analysis enables us to simultaneously study the functional and phylogenetic markers of hundreds of microorganisms which are involved in active bioremediation process in an environment. We have previously described development of a hybrid 60-mer multibacterial microarray platform (BiodegPhyloChip) for profiling the bacterial communities and functional genes simultaneously in environments undergoing active bioremediation process (Pathak et al; Appl Microbiol Biotechnol,Vol. 90, 1739-1754). The present study involved profiling the status of bacterial communities and functional (biodegradation) genes using the developed 60-mer oligonucleotide microarray BiodegPhyloChip at five contaminated hotspots in the state of Gujarat, in western India. The expression pattern of functional genes (coding for key enzymes in active bioremediation process) at these sites was studied to understand the dynamics of biodegradation in the presence of diverse group of chemicals. The results indicated that the nature of pollutants and their abundance greatly influence the structure of bacterial communities and the extent of expression of genes involved in various biodegradation pathways. In addition, site specific factors also play a pivotal role to affect the microbial community structure as was evident from results of 16S rRNA gene profiling of the five contaminated sites, where the community structure varied from one site to another drastically.
2012-12-01 | GSE38004 | GEO
Project description:To find out which miRNAs are significantly differential expression and potentially involved in the process of inflammation promoting carcinogenesis of colorectal cancer (CRC). We established a colitis-associated CRC (AOM/DSS, Azoxymethane/Dextran sulfate sodium salt) model, colitis (DSS) model and high dose carcinogen (AOM, about 5 times AOM amount given than AOM/DSS model) model. At day 100 when tumor formed in AOM/DSS bearing mice (colitis-associated CRC mice) but no tumor was found in AOM (high dose carcinogen) and DSS model, we employed miRNA microarray as a discovery platform to identify genes with the potential to involve in the progression of CRC promoted by inflammation.
2013-05-10 | GSE44983 | GEO
Project description:Understanding the bacterial community structure, and their functional analysis for active bioremediation process is essential to design better and cost effective strategies. Microarray analysis enables us to simultaneously study the functional and phylogenetic markers of hundreds of microorganisms which are involved in active bioremediation process in an environment. We have previously described development of a hybrid 60-mer multibacterial microarray platform (BiodegPhyloChip) for profiling the bacterial communities and functional genes simultaneously in environments undergoing active bioremediation process (Pathak et al; Appl Microbiol Biotechnol,Vol. 90, 1739-1754). The present study involved profiling the status of bacterial communities and functional (biodegradation) genes using the developed 60-mer oligonucleotide microarray BiodegPhyloChip at five contaminated hotspots in the state of Gujarat, in western India. The expression pattern of functional genes (coding for key enzymes in active bioremediation process) at these sites was studied to understand the dynamics of biodegradation in the presence of diverse group of chemicals. The results indicated that the nature of pollutants and their abundance greatly influence the structure of bacterial communities and the extent of expression of genes involved in various biodegradation pathways. In addition, site specific factors also play a pivotal role to affect the microbial community structure as was evident from results of 16S rRNA gene profiling of the five contaminated sites, where the community structure varied from one site to another drastically. Agilent one-color CGH experiment and one-color Gene Expresssion expereiment,Organism: Genotypic designed Agilent-17159 Genotypic designed Agilent Multibacterial 8x15k Array , Labeling kits: Agilent Genomic DNA labeling Kit (Part Number: 5190-0453) and Agilent Quick Amp Kit PLUS (Part number: 5190-0442).
2012-12-01 | E-GEOD-38004 | biostudies-arrayexpress
Project description:To find out which miRNAs are significantly differential expression and potentially involved in the process of inflammation promoting carcinogenesis of colorectal cancer (CRC). We established a colitis-associated CRC (AOM/DSS, Azoxymethane/Dextran sulfate sodium salt) model, colitis (DSS) model and high dose carcinogen (AOM, about 5 times AOM amount given than AOM/DSS model) model. At day 100 when tumor formed in AOM/DSS bearing mice (colitis-associated CRC mice) but no tumor was found in AOM (high dose carcinogen) and DSS model, we employed miRNA microarray as a discovery platform to identify genes with the potential to involve in the progression of CRC promoted by inflammation. 5-7 weeks female BALB/c mice, (1) AOM/DSS group: AOM 12.5mg/kg i.p. at day 1, DSS drinking 5d/21dx3circles from day 5; (2) AOM group: AOM 10mg/kg i.p. 1/weekx6 from day 1; (3) DSS group: DSS drinking 5d/21dx3circles from day 5. The distal colon epithelial tissues were collected at day100 when tumor formed in AOM/DSS bearing mice. The miRNA microarray experiments were performed together.
2013-05-10 | E-GEOD-44983 | biostudies-arrayexpress
Project description:To find out which mRNAs are significantly differential expression and potentially involved in the process of inflammation promoting carcinogenesis of colorectal cancer (CRC). We established a colitis-associated CRC (AOM/DSS, Azoxymethane/Dextran sulfate sodium salt) model, colitis (DSS) model and high dose carcinogen (AOM, about 5 times AOM amount given than AOM/DSS model) model. At day 100 when tumor formed in AOM/DSS bearing mice (colitis-associated CRC mice) but no tumor was found in AOM (high dose carcinogen) and DSS model, we employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to involve in the progression of CRC promoted by inflammation. 5-7 weeks female BALB/c mice, (1) AOM/DSS group: AOM 12.5mg/kg i.p. at day 1, DSS drinking 5d/21dx3circles from day 5; (2) AOM group: AOM 10mg/kg i.p. 1/weekx6 from day 1; (3) DSS group: DSS drinking 5d/21dx3circles from day 5. The distal colon epithelial tissues were collected at day100 when tumor formed in AOM/DSS bearing mice. The whole genome microarray expression profiling experiments were performed together.
2013-05-10 | E-GEOD-44904 | biostudies-arrayexpress
Project description:To find out which mRNAs are significantly differential expression and potentially involved in the process of inflammation promoting carcinogenesis of colorectal cancer (CRC). We established a colitis-associated CRC (AOM/DSS, Azoxymethane/Dextran sulfate sodium salt) model, colitis (DSS) model and high dose carcinogen (AOM, about 5 times AOM amount given than AOM/DSS model) model. At day 100 when tumor formed in AOM/DSS bearing mice (colitis-associated CRC mice) but no tumor was found in AOM (high dose carcinogen) and DSS model, we employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to involve in the progression of CRC promoted by inflammation.
2013-05-10 | GSE44904 | GEO
Project description:Bacterial community during treatments process Raw sequence reads
| PRJNA475822 | ENA