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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Microarray/gene expression analysis of RNA isolated with two different protocols from human blood sampled on PAXgene and Tempus.

ABSTRACT: Blood from four healthy volunteers was sampled on both PAXgene and Tempus tubes after two hours of fasting and abstention from coffee, medication and exercise. The content of each tube was split in two aliquotes where one aliquot was isolated using the sampling systems' original protocol and the second aliquot using a modified common protocol. The aim of this study was to establish a common RNA isolation protocol for these two systems and investigate if it could reduce the differences in gene expression.

ORGANISM(S): Homo sapiens

SUBMITTER: Anne Heidi Skogholt

PROVIDER: E-MTAB-5139 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Microarray/gene expression analysis of RNA isolated with two different protocols from human blood sampled on PAXgene and Tempus.

Project description:Blood from four healthy volunteers was sampled on both PAXgene and Tempus tubes after two hours of fasting and abstention from coffee, medication and exercise. The content of each tube was split in two aliquotes where one aliquot was isolated using the sampling systems' original protocol and the second aliquot using a modified common protocol. The aim of this study was to establish a common RNA isolation protocol for these two systems and investigate if it could reduce the differences in gene expression.

2017-04-01 | E-MTAB-5138 | biostudies-arrayexpress

Transcription profiling of human peripheral blood samples collected into PAXgene or Tempus tubes vs. the same 5 healthy control samples drawn in Li Heparin Differential gene expression profiles are dependent upon method of peripheral blood RNA isolation (direct, heparin

Project description:RNA isolation and purification steps greatly influence the results of gene expression profiling. There are two commercially available products for whole blood RNA collection, PAXgene and Tempus blood collection tubes, and each comes with their own RNA purification method. We examined the impact of RNA isolation methods on gene expression profiles. We demonstrated that peripheral blood RNA isoaltion can critically impact differential expression results, particularly in the clinical setting where fold-change differences are typically small and there is inherent variability within biological corhorts Experiment Overall Design: Comparison of 5 healthy control samples drawn directly in PAXgene or Tempus tubes vs. the same 5 healthy control samples drawn in Li Heparin tubes with no PHA stimulation.

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Transcription profiling of human peripheral blood samples using different collection protocols - superseries of GSE12709, GSE12710

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Project description:RNA isolation and purification steps greatly influence the results of gene expression profiling. There are two commercially available products for whole blood RNA collection, PAXgene and Tempus blood collection tubes, and each comes with their own RNA purification method. We examined the impact of RNA isolation methods on gene expression profiles. We demonstrated that peripheral blood RNA isoaltion can critically impact differential expression results, particularly in the clinical setting where fold-change differences are typically small and there is inherent variability within biological corhorts Experiment Overall Design: Whole blood from 7 healthy individuals was collected using Li Heparin tubes, and was incubated for 3 hours at room temperature with or without addition of 25 ug/mL of PHA. After incubation, samples were subsequently transferred to either Tempus or PAXgene tubes.

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Baseline expression of symptomatic and asymptomatic subjects after YF17D vaccination in Trial 1

Project description:This study investigates how the baseline expression level of genes impact symptomatic outcome of flaviviral infection. Before given the YF17D vaccine, whole blood was extracted into tempus tubes from vaccinated subjects. Thereafter, the subjects were assessed if they experienced adverse events (or symptoms). 27 subjects (n=19 symptomatic, n=8 asymptomatic) were processed according to manufacturer's protocol. Transcript expression was then evaluated by Affymetrix Human GeneChip 2.0 ST array, performed at Duke-NUS Genome Biology Core Facility. Data analysis and processing was performed using Partek software and enriched pathways determined by Reactome database from Enrichr.

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Project description:The autosomal recessive immuno-osseus dysplasia spondyloenchondrodysplasia (SPENCD) is characterised by the variable combination of metaphyseal and vertebral bone lesions, immune dysfunction with features of both autoimmunity and immunodeficiency, and neurological involvement including developmental delay and spasticity with intracranial calcification and leukodystrophy. This transcription profiling study of blood compared four patients to two control subjects. A deficiency of ACP5 encoding tartrate resistant acid phosphatase (TRAP) was found to cause this skeletal dysplasia demonstrating a type I interferon signature with autoimmunity.

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Cross-reactive antibodies enhance live attenuated virus infection for increased immunogenicity

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Transcription profiling of Paxgene collected human whole blood and hematopoietic lineages

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