Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6787150.fastq.gz | Fastqsanger.gz | |||
| SRR6787160.fastq.gz | Fastqsanger.gz | |||
| SRR6787170.fastq.gz | Fastqsanger.gz | |||
| SRR6787180.fastq.gz | Fastqsanger.gz | |||
| SRR6787190.fastq.gz | Fastqsanger.gz |
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Project description:RNA transfer via extracellular vesicles (EVs) influences cell phenotypes; however, lack of information regarding biogenesis of RNA-containing EVs has limited progress in the field. Here, we identify endoplasmic reticulum membrane contact sites (ER MCS) as platforms for generation of RNA-containing EVs. We identify a subpopulation of small EVs that is highly enriched in RNA and regulated by the ER MCS linker protein VAP-A. Functionally, VAP-A-regulated EVs are critical for miR-100 transfer between cells and in vivo tumor formation. Lipid analysis of VAP-A-knockdown EVs revealed reductions in the EV biogenesis lipid ceramide. Knockdown of the VAP-A-binding ceramide transfer protein CERT led to similar defects in EV RNA content. Imaging experiments revealed that VAP-A promotes lumenal filling of multivesicular bodies (MVBs). CERT localizes to MVBs, and the ceramide-generating enzyme neutral sphingomyelinase 2 colocalizes with VAP-A-positive ER. We propose that ceramide transfer via VAP-A-CERT linkages drives biogenesis of a select RNA-containing population.
2022-04-05 | GSE188223 | GEO
Project description:We preformed a systems biological assessment of lower respiratory tract host immune responses and microbiome dynamics in COVD-19 patients, using bulk RNA-sequencing, single-cell RNA sequencing, and techniques, and microbiome analysis. Are focus was on differential gene expression in severe COVID-19 patients who developed ventilator associated pneumonia (VAP) during their course versus severe COVID-19 patients who did not develop VAP. We found early impairment in antibacterial immune signaling in patients two or more weeks prior to the development of VAP, compared to COVID-19 patients who did not develop VAP. There was no signficant difference in viral load, but an association of disruption in lung microbiome by alpha and beta diversity metrics was also found.
2021-03-03 | GSE168018 | GEO
Project description:We preformed a systems biological assessment of lower respiratory tract host immune responses and microbiome dynamics in COVD-19 patients, using bulk RNA-sequencing, single-cell RNA sequencing, and techniques, and microbiome analysis. Are focus was on differential gene expression in severe COVID-19 patients who developed ventilator associated pneumonia (VAP) during their course versus severe COVID-19 patients who did not develop VAP. We found early impairment in antibacterial immune signaling in patients two or more weeks prior to the development of VAP, compared to COVID-19 patients who did not develop VAP. There was no signficant difference in viral load, but an association of disruption in lung microbiome by alpha and beta diversity metrics was also found.
2021-03-03 | GSE168017 | GEO
Project description:Vascular adhesion protein-1 (VAP-1) is an endothelial cell-surface protein. It is also an enzyme posessing semicarbazide-sensitive amine oxidase activity (EC.1.4.3.6). VAP-1 is involved in leukocyte traffic. To study the role of VAP-1 in tumor immunity, we compared gene expression profiles in melanomas growing in VAP-1 -/- mice and their wid-type littermates.
2009-10-27 | GSE13626 | GEO
Project description:Objective: Identify genes that are differentially expressed between critically ill trauma patients who go on to develop ventilator-associated pneumonia (VAP) compared to similar patients who do not develop VAP Using gene expression differences, develop a model that predicts which patients are at greater risk of developing VAP.
2013-01-01 | GSE30385 | GEO
Project description:INTRO: The ongoing challenge of accurately diagnosing infection in the ICU motivates a search for novel molecular diagnostics. In the current study, we tested the hypothesis that the informational content of circulating leukocytes differs, thereby allowing one to rank leukocyte populations on their potential to contribute to RNA diagnostics for pneumonia. METHODS: Sixteen patients (10 male, 6 female) at risk for VAP were entered into our IRB-approved study that collects blood and clinical data every 48 hours for up to 21 days. Four of the sixteen patients developed VAP as diagnosed and treated by the attending ICU physician. Previously reported blood protocols were used to isolate buffy coat, enriched neutrophil, and enriched monocyte populations by using negative selection. Cellular purity was assessed by FACS for one of the 4 VAP patients. Genome-wide expression analysis was performed on RMA-normalized signal from Affymetrix U133 2.0 Plus GeneChips. EDGE software (FDR=0.10) was used to determine changes in mRNA abundance over time for each cell population. RESULTS: During the 5-day window in which each of the four patients (all males) developed VAP, significant changes in gene expression were observed (Table 2), but the information content (number of genes altered) varied across leukocyte populations. These differences were not due to signal variance (coefficient of variation, CV) or differences in the number of samples available for analysis. Moreover, only 0.6% of the monocyte gene list overlaps with the neutrophil list, arguing that neutrophil contamination of monocyte populations is insufficient to explain the 40-fold difference in gene number. CONCLUSIONS: Enriched monocyte populations from circulating blood provide far more genes for study of the host response to VAP than the other 2 cell populations studied. This information should be considered when designing blood gene expression profiling experiments in patients at risk for sepsis. Keywords: time course Four patients over several timepoints measured three different cell types for VAP signal
2010-09-08 | E-GEOD-12838 | biostudies-arrayexpress
Project description:Vascular adhesion protein-1 (VAP-1) is an endothelial cell-surface protein. It is also an enzyme posessing semicarbazide-sensitive amine oxidase activity (EC.1.4.3.6). VAP-1 is involved in leukocyte traffic. To study the role of VAP-1 in tumor immunity, we compared gene expression profiles in melanomas growing in VAP-1 -/- mice and their wid-type littermates. The B16-F10-Luc-G5 melanoma cells (Xenogen) were injected subcutaneously into abdominal area of 2 wild-type and 2 VAP-1 -/- mice. Tumors were grown until day 10 when mice were euthanized. Tumors were dissected and total RNA was isolated using the Qiagen RNA extraction kit.
2010-04-07 | E-GEOD-13626 | biostudies-arrayexpress
Project description:INTRO: The ongoing challenge of accurately diagnosing infection in the ICU motivates a search for novel molecular diagnostics. In the current study, we tested the hypothesis that the informational content of circulating leukocytes differs, thereby allowing one to rank leukocyte populations on their potential to contribute to RNA diagnostics for pneumonia. METHODS: Sixteen patients (10 male, 6 female) at risk for VAP were entered into our IRB-approved study that collects blood and clinical data every 48 hours for up to 21 days. Four of the sixteen patients developed VAP as diagnosed and treated by the attending ICU physician. Previously reported blood protocols were used to isolate buffy coat, enriched neutrophil, and enriched monocyte populations by using negative selection. Cellular purity was assessed by FACS for one of the 4 VAP patients. Genome-wide expression analysis was performed on RMA-normalized signal from Affymetrix U133 2.0 Plus GeneChips. EDGE software (FDR=0.10) was used to determine changes in mRNA abundance over time for each cell population. RESULTS: During the 5-day window in which each of the four patients (all males) developed VAP, significant changes in gene expression were observed (Table 2), but the information content (number of genes altered) varied across leukocyte populations. These differences were not due to signal variance (coefficient of variation, CV) or differences in the number of samples available for analysis. Moreover, only 0.6% of the monocyte gene list overlaps with the neutrophil list, arguing that neutrophil contamination of monocyte populations is insufficient to explain the 40-fold difference in gene number. CONCLUSIONS: Enriched monocyte populations from circulating blood provide far more genes for study of the host response to VAP than the other 2 cell populations studied. This information should be considered when designing blood gene expression profiling experiments in patients at risk for sepsis. Keywords: time course
2010-09-09 | GSE12838 | GEO
Project description:Objective: Identify genes that are differentially expressed between critically ill trauma patients who go on to develop ventilator-associated pneumonia (VAP) compared to similar patients who do not develop VAP Using gene expression differences, develop a model that predicts which patients are at greater risk of developing VAP. Prospective observational study, analysis of gene expression in 20 patient samples, 10 that developed ventilator-associated pneumonia, 10 that did not
2013-01-01 | E-GEOD-30385 | biostudies-arrayexpress
Project description:The onset of an infection-specific transcriptional program precedes the clinical diagnosis in patients who developed Ventilator-associated pneumonia (VAP). Ventilator-associated tracheobronchitis (VAT) is another respiratory infection affecting<br><br>outcomes in intubated patients, but interactions between VAT and VAP remains unknown.
2011-11-19 | E-MEXP-3001 | biostudies-arrayexpress