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The impact of the anticoagulant type in blood collection tubes on circulating plasma miRNA profiles revealed by small RNA sequencing

ABSTRACT: The impact of the anticoagulant type in blood collection tubes on circulating plasma miRNA profiles revealed by small RNA sequencing

PROVIDER: PRJNA827783 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18791535.fastq.gz	Fastqsanger.gz
	SRR18791536.fastq.gz	Fastqsanger.gz
	SRR18791537.fastq.gz	Fastqsanger.gz
	SRR18791538.fastq.gz	Fastqsanger.gz
	SRR18791539.fastq.gz	Fastqsanger.gz

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The impact of the anticoagulant type in blood collection tubes on circulating plasma miRNA profiles revealed by small RNA sequencing

Project description:Pre-analytic factors have a significant influence on circulating miRNA profiling. The aim of this study was the comprehensive NGS-based assessment of the impact of anticoagulant type in blood collection tubes on circulating plasma miRNA profiles.

2022-09-07 | GSE200970 | GEO

Towards clinical applications of blood-born miRNA signatures: The influence of the anticoagulant EDTA on miRNA abundance

2015-12-31 | GSE73401 | GEO

The Impact of the Anticoagulant Type in Blood Collection Tubes on Circulating Extracellular Plasma MicroRNA Profiles Revealed by Small RNA Sequencing.

Project description:Pre-analytical factors have a significant influence on circulating microRNA (miRNA) profiling. The aim of this study was a comprehensive assessment of the impact of the anticoagulant type in blood collection tubes on circulating plasma miRNA profiles using small RNA sequencing. Blood from ten healthy participants (five males and five females from 25 to 40 years old) was taken in collection tubes with four different anticoagulants: acid citrate dextrose (ACD-B), sodium citrate, citrate-theophylline-adenosine-dipyridamole (CTAD) and dipotassium-ethylenediaminetetraacetic acid (K2 EDTA). Platelet-free plasma samples were obtained by double centrifugation. EDTA plasma samples had elevated levels of hemolysis compared to samples obtained using other anticoagulants. Small RNA was extracted from plasma samples and small RNA sequencing was performed on the Illumina NextSeq 500 system. A total of 30 samples had been successfully sequenced starting from ~1 M reads mapped to miRNAs, allowing us to analyze their diversity and isoform content. The principal component analysis showed that the EDTA samples have distinct circulating plasma miRNA profiles compared to samples obtained using other anticoagulants. We selected 50 miRNA species that were differentially expressed between the sample groups based on the type of anticoagulant. We found that the EDTA samples had elevated levels of miRNAs which are abundant in red blood cells (RBC) and associated with hemolysis, while the levels of some platelet-specific miRNAs in these samples were lowered. The ratio between RBC-derived and platelet-derived miRNAs differed between the EDTA samples and other sample groups, which was validated by quantitative PCR. This study provides full plasma miRNA profiles of 10 healthy adults, compares them with previous studies and shows that the profile of circulating miRNAs in the EDTA plasma samples is altered primarily due to an increased level of hemolysis.

| S-EPMC9499385 | biostudies-literature

Towards clinical applications of blood-born miRNA signatures: The influence of the anticoagulant EDTA on miRNA abundance

Project description:Circulating microRNAs (miRNAs) from blood are increasingly recognized as biomarker candidates for human diseases. Clinical routine settings frequently include blood sampling in tubes with EDTA as anticoagulant without considering the influence of phlebotomy on the overall miRNA expression pattern. We collected blood samples from six healthy individuals each in an EDTA blood collection tube. Subsequently, the blood was transferred into PAXgeneTM tubes at three different time points, i.e. directly (0 min), 10 min, and 2 h after phlebotomy. As control blood was also directly collected in PAXgeneTM blood RNA tubes that contain a reagent to directly lyse blood cells and stabilize their content. For all six blood donors at the four conditions (24 samples) we analyzed the abundance of 1,205 miRNAs by human Agilent miRNA V16 microarrays. Blood from 6 healthy individuals was collected in one PAXgeneTM blood RNA tube (Becton Dickinson, 2.5 ml blood) and one dipotassium EDTA blood tube (EDTA-KE Monovette, Sarstedt, 9 ml blood) per individual. There was no known disease for any of the blood donors. A fixed volume of 2.5 ml blood from the EDTA tube was transferred at three different time points after blood withdrawal (0 min, 10 min, and 2 h) into fresh PAXgene blood RNA tubes to ensure stabilization of the RNA in the blood samples. All PAXgene blood tubes were stored at room temperature until at least 2 h after the last transfer of EDTA blood into PAXgene tubes, to ensure complete lysis of the blood cells, before they were stored at -20Â°C until RNA isolation.

2015-12-31 | E-GEOD-73401 | biostudies-arrayexpress

Translatome of floral buds, in vivo pollinated pollen tubes, and in vitro cultured pollen grains/tubes from LAT52-HF-RPL18 Arabidopsis

2014-02-01 | GSE43299 | GEO

Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome

Project description:In this study, we evaluated the effect of preservation agent on the effect of the methylation pattern of cell-free DNA. The methylation pattern was assessed with cell-free reduced representation sequencing (cf-RRBS). Blood was drawn from three healthy individuals (male and females between 24 and 50 years old). 15 tubes were drawn per healthy volunteer: 3x BD Vacutainer K2E EDTA spray tubes (REF 367525), 3x Streck Cell-Free DNA BCT tubes (catalogue number 218962), 3x PAXgene Blood ccfDNA tubes (catalogue number 768115), 3x Roche Cell-Free DNA Collection tubes (catalogue number 07785674001) and 3x Biomatrica LBgard blood tubes (SKU 68021-001), resulting in 45 samples in total. All 45 samples were sequenced on a NovaSeq6000. Samples are given as bismark coverage files (GRCh37).

2020-04-03 | E-MTAB-8858 | biostudies-arrayexpress

Comparison of cell stabilizing blood collection tubes for circulating plasma tumor DNA.

Project description:ObjectivesCirculating plasma DNA is being increasingly used for biomedical and clinical research as a substrate for genetic testing. However, cell lysis can occur hours after venipuncture when using standard tubes for blood collection, leading to an increase in contaminating cellular DNA that may hinder analysis of circulating plasma DNA. Cell stabilization agents can prevent cellular lysis for several days, reducing the need for immediate plasma preparation after venipuncture, thereby facilitating the ease of blood collection and sample preparation for clinical research. However, the majority of cell stabilizing reagents have not been formally tested for their ability to preserve circulating plasma tumor DNA.Design & methodsIn this study, we compared the properties of two cell stabilizing reagents, the cell-free DNA BCT tube and the PAXgene tube, by collecting blood samples from metastatic breast cancer patients and measuring genome equivalents of plasma DNA by droplet digital PCR. We compared wild type PIK3CA genome equivalents and also assayed for two PIK3CA hotspot mutations, E545K and H1047R.ResultsOur results demonstrate that blood stored for 7 days in BCT tubes did not show evidence of cell lysis, whereas PAXgene tubes showed an order of magnitude increase in genome equivalents, indicative of considerable cellular lysis.ConclusionsWe conclude that BCT tubes can prevent lysis and cellular release of genomic DNA of blood samples from cancer patients when stored at room temperature, and could therefore be of benefit for blood specimen collections in clinical trials.

| S-EPMC4600652 | biostudies-literature

Benchmarking blood collection tubes and processing intervals for extracellular vesicle performance metrics

Project description:Extracellular vesicle (EV) analysis from blood samples is under intense investigation and holds the potential to deliver clinically meaningful biomarkers for health and disease. Technical variation must be minimized to confidently assess EV-associated biomarkers but the impact of pre-analytics on EV characteristics in blood samples remains minimally explored. We present the results from the first large-scale EV Blood Benchmarking (EVBB) study in which we systematically compared 11 blood collection tubes (BCT; 6 preserving and 5 non-preserving) and 3 blood processing intervals (BPI; 1h, 8h and 72h) on defined performance metrics (n=9). The EVBB study identifies a significant impact of multiple BCT and BPI on a diverse set of metrics reflecting blood sample quality, ex-vivo generation of blood-cell derived EV, EV recovery and EV-associated molecular signatures. The results assist the informed selection of the optimal BCT and BPI for EV analysis. The proposed metrics serve as a platform to guide future research on EV pre-analytics and further support methodological standardization of EV studies.

2023-03-13 | PXD035199 | Pride

Translatome of floral buds, in vivo pollinated pollen tubes, and in vitro cultured pollen grains/tubes from LAT52-HF-RPL18 Arabidopsis

Project description:Little is known of the transcriptome of in vivo-grown pollen tubes, due to the difficulty of collection of pollen tubes elongating within the maternal gynoecium.We obtained the mRNAs undergoing translation (the translatome) of in vivo-grown pollen tubes from self-pollinated gynoecia of Arabidopsis thaliana(Col-0). Transgenic Arabidopsis plants (LAT52-HF-RPL18) harboring an epitope tagged ribosomal protein L18 driven by the pollen specific promoter (ProLAT52) were used for mRNA-ribosome complex isolation. After collection of polyribosomal (polysomal) complexes from self-pollinated (in vivo), unpollinated styles (buds), and in vitro-cultured pollen tubes, the actively translated mRNAs (the translatome) were purified, amplified to antisense RNA (aRNA). These aRNAs were hybridized to microarrays.Three independent biological replicates samples of aRNA from Bud, in vivo, and in vitro polysomal mRNA (translatomes) were hybridized to GeneChips to produce CEL files.

2014-02-01 | E-GEOD-43299 | biostudies-arrayexpress

Proteomic analysis of secretions from pollen tubes and ovaries of Camellia oleifera cultured semi-in vivo

Project description:Self-inhibition of pollen tubes plays a key role in SI, but the underlying mechanism in Camellia oleifera is poorly understood. Collection of secreted proteins from Camellia oleifera pollen tubes and ovaries for high-throughput sequencing.

2023-03-11 | PXD035406 | Pride

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