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Affymetrix SNP array data for DNA copy number analysis of supernatant DNA

ABSTRACT: DNA contained in the supernatant of cultured malignant cells as well as from plasma/serum of cancer patients is able to transform recipient immortal murine NIH3T3 cells. We demonstrate for the first time that human circulating DNA is able to drive tumor progression in an immunocompetent colon carcinogenesis rat model and that treatment with DNAse I/proteases has antitumor effects in a xenograft nude mice model. DNA copy number analysis of the DNA purifed from the supernatat of SW480 cell cultures was analyzed to determine if specific regions of the genome are represented in this fraction.

ORGANISM(S): Homo sapiens

PROVIDER: GSE35052 | GEO | 2012/07/09

SECONDARY ACCESSION(S): PRJNA150843

REPOSITORIES: GEO

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Affymetrix SNP array data for DNA copy number analysis of supernatant DNA

Project description:DNA contained in the supernatant of cultured malignant cells as well as from plasma/serum of cancer patients is able to transform recipient immortal murine NIH3T3 cells. We demonstrate for the first time that human circulating DNA is able to drive tumor progression in an immunocompetent colon carcinogenesis rat model and that treatment with DNAse I/proteases has antitumor effects in a xenograft nude mice model. DNA copy number analysis of the DNA purifed from the supernatat of SW480 cell cultures was analyzed to determine if specific regions of the genome are represented in this fraction. We hybridized genomic DNA from parental SW480 cells, the DNA isolated from supernatant of SW480 cells, onto the 500K Affymetrix genotyping array set, following the manufacturer´s instructions, and compared their DNA copy number profile against a common reference generated using data from the International HapMap project.

2012-07-08 | E-GEOD-35052 | biostudies-arrayexpress

Epithelial cells in contact with bacterial supernatant

Project description:Epithelial cells were in contact with bacteria supernatant during different times of incubation. time course supernatant 10 % MM39 Keywords: time-course

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Whole transcriptomes analyses of HEK293FT cell line treated with ISLR secreted supernatant or empty vector control supernatant

Project description:Purpose: To explore the molecular mechanisms of ISLR protein, RNA sequencing was performed to analyze the geome-wide change of ISLR secreted supernatant treated HEK293FT cells compared to those of control supernatant treated cells. Methods: Total mRNA was extracted from HEK293FT cells in triplicate respectively. Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina Hiseq 4000 platform. As a reasult, we got the transcript data using Hisat2 followed by Stringtie. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: We mapped about 60 million sequence reads per sample to the human genome and identified about 58,000 transcripts in HEK293FT cells. Many transcripts showed different expression between ISLR secreted supernatant and control treated HEK293FT cells, with a fold change ≥2 and p value <0.05. Gene set enrichment analysis (GSEA) showed a significantly positive enrichment of Hippo target genes. Conclusion: Our study present the datiled transcripts analysis of HEK293FT cells, with biologic replicates. Based on RNA-seq transcriptome characterization , we conclude a molecular mechanism of ISLR regulating multiple pathways related to tissue repair.

2020-03-20 | GSE135280 | GEO

RNA-seq Analysis of Enterococcus faecalis in Response to Bacillus subtilis natto Supernatant Treatment

Project description:We found that biofilm formation ability of E. faecalis was impacted by culture supernatant of probiotic B. subtilis natto. To further understand how E. faecalis responded to B. subtilis natto supernatant, we searched for differentially expressed genes between E. faecalis treated with or without B. subtilis natto supernatant using RNA-seq analysis.

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Transcriptome and translatome of killing supernatant cultured human monocytes

Project description:To investigate whether metoprolol treatment could affect the transcriptome and translatome of killing supernatant cultured human monocytes

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Pseudomonas aeruginosa gene regulation by Staphylococcus aureus supernatant or added secreted products

Project description:Pseudomonas aeruginosa and Staphylococcus aureus are often co-isolated in persistent infections. The goal of this study was to determine how secreted products that were identified in S. aureus supernatant affect gene expression in P. aeruginosa. Therefore, media control, the indicated products in media, or S. aureus supernatant was added to P. aeruginosa cultures at 25% total volume and gene expression was measured at 20 min and 2 h using RNA-seq. The individual products induced distinct pathways in P. aeruginosa. The products in combination recapitulated much of the differential gene expression seen in P. aeruginosa in response to S. aureus supernatant.

2022-05-18 | GSE186138 | GEO

interaction with bacteria or bacterial supernatant

Project description:Epithelial cells were in contact either with live bacteria (S. aureus) or with bacterial supernatant during 3 hours. Three dependant experiment for each condition were performed. RNA from epithelial cells were extracted. Each condition was hybridized on 6 slides (3 slides with their corresponding swap) Keywords: parallel sample

2004-10-23 | GSE1853 | GEO

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