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RNA expression analysis of cells producing the synthetic protein DX over a 4hr time course

ABSTRACT: We expressed the man-made protein DX in E. coli cells over the course of 4 hours and examined effects on global gene expression.

ORGANISM(S): Escherichia coli

PROVIDER: GSE17568 | GEO | 2010/07/21

SECONDARY ACCESSION(S): PRJNA118673

REPOSITORIES: GEO

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RNA expression analysis of cells producing the synthetic protein DX over a 4hr time course

Project description:We expressed the man-made protein DX in E. coli cells over the course of 4 hours and examined effects on global gene expression. We analyzed the change in RNA expression profiles of E. coli cells expressing the synthetic protein DX every half-hour over a four hour experiment. These samples were compared to un-induced control cells. Each sample represents a different time point with the 647nm channel being the DX-expressing samples and the 555nm chanel being the un-induced controls. Controls contained the DX cassette in the pBAD18 vector and were treated identically to the experimental cells, except the arabinose inducer was omitted from the growth media. The 2.5 hour time point is omitted because the control cDNA failed to label properly. No dye swaps or repeats were performed because: a) we were examining trends over time and any anomalous or faulty spot would be excluded during analysis if it were not part of a general trend, and b) Microarray data is not being used to draw conclusions, but rather to draw a picture of what was changing in the cell and open up avenues of exploration.

2010-07-21 | E-GEOD-17568 | biostudies-arrayexpress

Leptospirillum ferriphilum strain:DX

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Sulfobacillus thermosulfidooxidans strain:DX

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Acidithiobacillus caldus strain:DX

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Leptospirillum ferriphilum strain:DX

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Rhodopseudomonas palustris DX-1

Project description:Rhodopseudomonas palustris DX-1 genome sequencing project

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BreastPRS is a Gene Expression Assay that Stratifies Intermediate-Risk Oncotype DX Patients into High or Low-Risk for Disease Recurrence

Project description:Molecular prognostic assays, such as Oncotype DX, are increasingly incorporated into the management of patients with invasive breast carcinoma. BreastPRS is a new molecular assay developed and validated from a meta-analysis of publically available genomic datasets. We applied the assay to matched fresh-frozen (FF) and formalin-fixed paraffin embedded (FFPE) tumor samples to translate the assay to FFPE. A linear relationship of the BreastPRS prognostic score was observed between tissue preservation formats. BreastPRS recurrence scores were compared with Oncotype DX recurrence scores from 246 patients with invasive breast carcinoma and known Oncotype DX results. Using this series, a 120-gene linear discriminant algorithm (LDA) was trained to predict Oncotype DX risk groups and then applied to series of untreated, node-negative, estrogen receptor (ER) – positive patients from previously published studies with known clinical outcomes. Correlation of recurrence score and risk group between Oncotype DX and BreastPRS was statistically significant (P<0.0001). 59 of 260 (23%) patients from four previously published studies were classified as intermediate-risk when the 120-gene LDA was applied. BreastPRS reclassified the 59 patients into binary risk groups (high vs. low-risk). 23 (39%) patients were classified as low-risk 36 (61%) as high-risk [P=0.029, HR: 3.64, 95% CI: 1.40 to 9.50]. At 10 years from diagnosis, the low-risk group had a 90% recurrence-free survival (RFS) rate, compared to 60% for the high-risk group. BreastPRS recurrence score is comparable to Oncotype DX and can reclassify Oncotype DX intermediate-risk patients into two groups with significant differences in RFS. Further studies are needed to validate these findings.

2013-06-23 | GSE47109 | GEO

BreastPRS is a Gene Expression Assay that Stratifies Intermediate-Risk Oncotype DX Patients into High or Low-Risk for Disease Recurrence

2013-06-23 | E-GEOD-47109 | biostudies-arrayexpress

Acidicaldus organivorans strain:DX-1

Project description:Acidicaldus organivorans strain:DX-1 Genome sequencing and assembly

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the Serum Metabolite Based PrecogColo Dx Test for Advanced Colorectal Neoplasia Screening

Project description:This study is to Evaluate the diagnostic sensitivity of the serum metabolite based PrecogColo Dx test for advanced colorectal neoplasia Screening, including advanced adenoma and colorectal cancer. There are two steps in this study. Firstly, the diagnostic model is established based on tumor-specific and gut-microbiome related serum metabolites. Secondly, the sensitivity, specificity and accuracy of the diagnostic model is evaluated in detecting advanced adenoma and colorectal cancer stages in an independent multi-centered cohort.

| 60956 | ecrin-mdr-crc

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