Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA133395 | ENA |
REPOSITORIES: ENA
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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
Project description:This SuperSeries is composed of the following subset Series: GSE24753: Genome-wide analysis of the effect of cryopreservation on peripheral blood mononuclear cells GSE24755: Genome-wide analysis of the effect of long-term cryopreservation on peripheral blood mononuclear cells GSE24757: Genome-wide analysis of the effect of long-term freezing of PAXgene Blood RNA tubes Refer to individual Series
2011-07-21 | E-GEOD-24758 | biostudies-arrayexpress
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. Total RNA was obtained from peripheral whole blood samples collected in PAXgene RNA tubes of healthy human subjects. RNA was either isolated after 24h storage at room temperature or after freezing of PAXgene RNA tubes for up to 1 year (6 weeks, 6 months and 12 months).
2011-07-21 | E-GEOD-24757 | biostudies-arrayexpress
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
Project description: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.
2016-11-15 | GSE89021 | GEO
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
Project description:Peripheral blood is an accessible and informative source of transcriptomal information for many human disease and pharmacogenomic studies. While there can be significant advantages to analyzing RNA isolated from whole blood, particularly in clinical studies, the preparation of samples for microarray analysis is complicated by the need to minimize artifacts associated with highly abundant globin RNA transcripts. The impact of globin RNA transcripts on expression profiling data can potentially be reduced by using RNA preparation and labeling methods that remove or block globin RNA during the microarray assay. We compared four different methods for preparing microarray hybridization targets from human whole blood collected in PAXGene tubes. Three of the methods utilized the Affymetrix one-cycle cDNA synthesis/in vitro transcription protocol but varied treatment of input RNA as follows: i. no treatment; ii. treatment with GLOBINclear; or iii. treatment with globin PNA oligos. In the fourth method cDNA targets were prepared with the Ovation amplification and labeling system. Results: We find that microarray targets generated with labeling methods that reduce globin mRNA levels or minimize the impact of globin transcripts during hybridization detect more transcripts in the microarray assay compared with the standard Affymetrix method. Comparison of microarray results with quantitative PCR analysis of a panel of genes from the NF-kappa B pathway shows good correlation of transcript measurements produced with all four target preparation methods, although method-specific differences in overall correlation were observed. The impact of freezing blood collected in PAXGene tubes on data reproducibility was also examined. Expression profiles show little or no difference when RNA is extracted from either fresh or frozen blood samples. Conclusion: RNA preparation and labeling methods designed to reduce the impact of globin mRNA transcripts can significantly improve the sensitivity of the DNA microarray expression profiling assay for whole blood samples. While blockage of globin transcripts during first strand cDNA synthesis with globin PNAs resulted in the best overall performance in this study, we conclude that selection of a protocol for expression profiling studies in blood should depend on several factors, including implementation requirements of the method and study design. RNA isolated from either freshly collected or frozen blood samples stored in PAXGene tubes can be used without altering gene expression profiles. Keywords: Whole Blood, Protocol Variation, Expression Profiling, Microarray, globin, PAXGene, PNA
2009-01-30 | GSE13292 | GEO
Project description:Detecting differential changes in the peripheral whole-blood transcriptome, post-challenge compared to pre-challenge; using globin reduced PAXgene (PAX.GR) tubes
2012-01-26 | GSE34158 | GEO
Project description:The objective of this analysis was to determine the transcriptional signature associated with experimental DENV-1 infection in human volunteers. Nine flavivirus naive volunteers were challenged with an attenuated DENV-1 strain - 45AZ5 - and blood collected for RNA extraction and transcriptional analysis on days 0, 8, 10, 14, and 28 post challenge using PAXgene collection tubes. Total RNA was isolated from the collection tubes and subjected to RNAseq analysis to identify genes and gene sets that were differentially expressed across the infection time course.
2022-08-30 | GSE182482 | GEO
Project description:The objective of this analysis was to determine the transcriptional signature associated with experimental primary DENV-3 infection in human volunteers. Nine flavivirus naive volunteers were challenged with an attenuated DENV-3 strain - CH53489 - and blood collected for RNA extraction and transcriptional analysis on or around study days 0, 6, 8, 10, 14, and 28 post challenge using PAXgene collection tubes. Total RNA was isolated from the collection tubes and subjected to RNAseq analysis to identify genes and gene sets that were differentially expressed across the infection time course.
2024-02-26 | GSE216328 | GEO