Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression in matched samples of peripheral whole blood collected and processed using the PAXgene vs Tempus system

ABSTRACT: To compare gene expression in whole blood samples collected in PAXgene RNA or Tempus collection tubes, and processed using the PAXgene Blood RNA Kit or Tempus Spin RNA isolation Kit, respectively.

ORGANISM(S): Homo sapiens

PROVIDER: GSE89021 | GEO | 2016/11/15

SECONDARY ACCESSION(S): PRJNA349808

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

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.

2008-11-13 | E-GEOD-12710 | biostudies-arrayexpress

Genome-wide analysis of the effect of long-term freezing of PAXgene Blood RNA tubes

Project description:Analysis of long-term freezing on the stability of transcriptome profiles in PAXgene stabilized whole blood samples. In the present study it was tested if long-term freezing of PAXgene RNA tubes (up to one year) has an influence on the transcriptome profile of peripheral whole blood samples. Results indicated that gene expression profiles of whole blood samples stabilized with PAXgene RNA tubes remain stable for at least 1 year.

2011-07-22 | GSE24757 | GEO

Transcription profiling of Paxgene collected human whole blood and hematopoietic lineages

Project description:Assessment of transcriptome stability in Paxgene collected whole blood and representation of hematopoietic lineages of whole blood transcriptome using single primer isothermal amplification probes without globin reduction protocols. As well as the stability assessment of Paxgene collected samples we investigated whether expression profiling of whole blood RNA (without globin reduction procedures) using the NuGEN single-primer isothermal amplification methods (which generate single stranded cDNA) allows faithful representation of individual lineages. ie. are we losing a lot of information by looking at whole blood rather than PBMCs or individual lineages. These 7 cell lineages were not stored in Paxgene tubes and are only for the purpose of querying the data generated from the Paxgene/sscDNA dataset (12 samples) in order to determine the representation of individual lineage transcriptomes in that dataset.

2008-06-30 | E-MEXP-1600 | biostudies-arrayexpress

Transcriptomic analysis of immune response in healthy controls and COVID-19 cases using the NanoString Human Immunology Panel

Project description:Daily transcriptomic profiling was conducted on whole blood collected from COVID-19 cases. Whole blood was collected in Tempus Blood RNA tubes, and RNA was extracted from whole blood using the Tempus Spin RNA Isolation Kit. Healthy controls consisted of participants of a measles, mumps and rubella re-vaccination study. Pre-vaccination whole blood was collected and processed and analyzed as above.

2020-03-27 | E-MTAB-8871 | biostudies-arrayexpress

Daily transcriptomic profiling of immune response in COVID-19 cases and healthy controls using the NanoString Human Immunology Panel

2021-02-24 | E-MTAB-9719 | biostudies-arrayexpress

Integrating whole blood transcriptomic collection procedures into the current anti-doping testing system, including long-term storage and re-testing of anti-doping samples

Project description:Recombinant human erythropoietin administration studies involving transcriptomic approaches have demonstrated a gene-expression signature that could aid detection of blood doping. However, current anti-doping testing does not involve blood collection into tubes with RNA preservative. This study investigated if whole blood in long-term storage and whole blood leftover from standard haematological testing in short-term storage could be used for transcriptomic analysis despite lacking RNA preservative. Whole blood samples were collected from thirteen and fourteen healthy males, for long-term and short-term storage experiments. Long-term storage: whole blood collected into Tempus™ tubes and K2EDTA tubes and subjected to long-term (i.e., −80°C) storage and RNA extracted. After storage, K2EDTA tubes were thawed and extracted using GeneJET RNA Purification Kit (Thermo Fisher Scientific, Vilnius, Lithuania) or Tempus™ Spin RNA Isolation Kit (Life Technologies, Carlsbad, CA, USA). RNA quality and purity was sufficient for gene expression analysis. Principle Component Analysis of microarray and RNA-seq gene expression data for long-term storage: When comparing gene expression between blood tubes with and without RNA preservation, 6% (4058 transcripts) were differentially expressed. RNA quantity, purity and integrity was not significantly compromised from long-term storage in blood storage tubes lacking RNA preservative, indicating that transcriptomic analysis could be conducted using anti-doping samples collected or biobanked without RNA preservation.

2021-08-13 | GSE181970 | GEO

Integrating whole blood transcriptomic collection procedures into the current anti-doping testing system, including long-term storage and re-testing of anti-doping samples [Long-term]

Project description:Purpose: Recombinant human erythropoietin administration studies involving “omics” approaches have demonstrated a gene-expression signature that could aid detection of blood doping. However, current anti-doping testing does not involve blood collection into tubes with RNA preservative. This study investigated if whole blood in long-term storage could be used for transcriptomic analysis despite lacking RNA preservation. Methods: Whole blood samples were collected from thirteen male healthy individuals. Long-term storage: whole blood collected into Tempus™ tubes and K2EDTA tubes and subjected to long-term (i.e., −80°C) storage and RNA extracted. After storage, Tempus and K2EDTA tubes were thawed and extracted using Tempus™ Spin RNA Isolation Kit (Life Technologies, Carlsbad, CA, USA). Samples from seven subjects that presented higher RIN value (≥7) were selected for RNA_Seq analysis. Results: The experiment provided RNA quality and purity for gene expression analysis. Total of 19239 genes were mapped and the gene expression analysis showed that 658 genes were differentially expressed (which means 3.4% of mapped genes). With 269 being up-regulated and 389 down-regulated. None of the transcripts described in previous studies as biomarkers for blood doping (Durussel et al. 2016; Wang, Durussel, et al. 2017) were differently expressed. Conclusion: RNA quantity, purity and integrity was not significantly compromised from long-term storage in blood storage tubes lacking RNA stabilisation, indicating that transcriptomic/omics analysis could be conducted using anti-doping samples collected or biobanked without RNA preservation.

2021-09-03 | GSE183073 | GEO

NanoString profiling of host response in healthy volunteers vaccinated with ARCT-021 self-amplifying mRNA vaccine or placebo

Project description:Transcriptomic profiling was conducted on whole blood collected from study participants (NCT04480957). A total of 106 healthy participants were randomized into single and two-injection cohorts. Gene transcript levels were determined at baseline (pre-dose 1), day 2, 3, and 8 for all vaccinees. In addition, gene expression was profiled at day 29 (pre-dose 2), 30 and 36 among vaccinees in the two-injection cohort. Whole blood was collected in Tempus Blood RNA tubes, and RNA was extracted from whole blood using the Tempus Spin RNA Isolation Kit.

2022-11-30 | E-MTAB-11315 | biostudies-arrayexpress

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

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

2017-04-01 | E-MTAB-5139 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data