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Comparison of collection strategies for germline analysis

ABSTRACT: Peripheral blood was collected from 3 patients in two types of tubes, EDTA and Streck. After removing plasma, DNA was extracted from the remaining blood and subjected to array profiling

ORGANISM(S): Homo sapiens

PROVIDER: GSE105032 | GEO | 2017/10/17

SECONDARY ACCESSION(S): PRJNA414452

REPOSITORIES: GEO

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Real-time quantitative PCR analysis of human stroke patients recovering from upper extremity hemiparesis

Project description:Fasting blood samples were collected from 27 stroke patients in EDTA tubes mean 19 days post-stroke, plasma was extracted and frozen at -80C, then 200uL of plasma sent for qPCR.

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The Extracellular RNA Quality Control (exRNAQC) study: Small RNA sequencing of blood collection tube study (exRNAQC013)

Project description:To evaluate the impact of blood collection tubes on extracellular RNA (exRNA) sequencing, 10 different blood collection tubes were compared by applying Small RNA sequencing (Illumina) to exRNA from human healthy donor plasma or serum. Three time spans between blood draw and downstream processing were evaluated for each of the tubes. Preservation tubes were processed immediately upon blood collection (T0), after 24 hours (T24), or after 72 hours (T72). Non-preservation plasma and serum tubes were processed immediately upon blood collection (T0), after 4 hours (T4), or after 16 hours (T16). Due to donor privacy concerns the raw data for this study have been submitted to the controlled-access archive EGA under the accession EGAS00001005263.

2021-06-10 | E-MTAB-10506 | biostudies-arrayexpress

The Extracellular RNA Quality Control (exRNAQC) study: RNA Exome sequencing of blood collection tube study (exRNAQC005)

Project description:To evaluate the impact of blood collection tubes on extracellular RNA (exRNA) sequencing, 10 different blood collection tubes were compared by applying RNA Exome sequencing (Illumina) to exRNA from human healthy donor plasma or serum. Three time spans between blood draw and downstream processing were evaluated for each of the tubes. Preservation tubes were processed immediately upon blood collection (T0), after 24 hours (T24), or after 72 hours (T72). Non-preservation plasma and serum tubes were processed immediately upon blood collection (T0), after 4 hours (T4), or after 16 hours (T16). Due to donor privacy concerns the raw data for this study have been submitted to the controlled-access archive EGA under the accession EGAS00001005263.

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

Project description:Background The methylation pattern of cfDNA, isolated from liquid biopsies, is gaining substantial interest for diagnosis and monitoring of diseases. We have evaluated the impact of type of blood collection tube and time delay between blood draw and plasma preparation on bisulfite-based cfDNA methylation profiling. Methods 15 tubes of blood were drawn from three healthy volunteer subjects (BD Vacutainer K2E EDTA spray tubes, Streck Cell-Free DNA BCT tubes, PAXgene Blood ccfDNA tubes, Roche Cell-Free DNA Collection tubes and Biomatrica LBgard blood tubes in triplicate). Samples were either immediately processed or stored at room temperature for 24 or 72 hours before plasma preparation. DNA fragment size was evaluated by capillary electrophoresis. Reduced representation bisulfite sequencing was performed on the cell-free DNA isolated from these plasma samples. We evaluated the impact of blood tube and time delay on several quality control metrics. Results All preservation tubes performed similar on the quality metrics that were evaluated. Furthermore, a considerable increase in cfDNA concentration and the fraction of it derived from NK cells was observed after a 72-hour time delay in EDTA tubes. Conclusion The methylation pattern of cfDNA is robust and reproducible in between the different preservation tubes. EDTA tubes processed as soon as possible, preferably within 24 hours, are the most cost effective. If immediate processing is not possible, preservation tubes are valid alternatives.

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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 collection strategies for germline analysis

Project description:Comparison of collection strategies for germline analysis

| PRJNA414452 | ENA

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Untargeted LC-MS to compare blood collection tube and processing time – HILIC & C18

Project description:Blood was collected from three healthy volunteers in 3 blood collection tubes: serum separator tube SST (serum), EDTA (plasma), and P100 (plasma) and stored at 4 degrees for 0, 0.5, 1, 2, 4, and 24 hours prior to centrifugation. Compounds were extracted using liquid-liquid extraction to obtain a hydrophilic and a hydrophobic fraction and analyzed using liquid chromatography mass spectrometry. Differences among the blood collection tubes and sample processing time were evaluated (ANOVA with Bonferroni FWER ≤ 0.05 and ANOVA with Benjamini Hochberg FDR ≤ 0.1, respectively).

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Analysis of tetraspanin distribution on plasma and serum extracellular vesicles indicates that separate subpopulations carries CD9, CD63 and CD81

Project description:The ability to isolate extracellular vesicles (EVs) from blood is vital in the development of EVs as disease biomarkers. Both serum and plasma can be used, but few studies have compared these sources in terms of the quantity and type of EVs that are obtained. The aim of this study was therefore to determine the presence of different subpopulations of EVs in plasma and serum. Blood samples were collected from healthy subjects, from which plasma and serum were isolated in parallel. ACD-A or EDTA tubes were used for the collection of plasma, while serum was obtained in clot activator tubes. We previously developed a method utilising a combination of density cushion and size exclusion chromatography to isolate EVs from plasma with minimal contamination of lipoprotein particles. In the current study, we applied this method to both EDTA-plasma and serum. In addition, EVs were isolated by a combination of density cushion and density gradient or by bead immune capturing (anti-CD63, anti-CD9, and anti-CD81 beads). The subpopulations of EVs were analysed by nanoparticle tracking analysis, Western blot, single particle interferometric reflectance imaging sensing, conventional and nano flow cytometry, magnetic bead enzyme-linked immunosorbent assay, and mass spectrometry.This study shows that a larger number of CD9+ EVs are present in EDTA-plasma compared to ACD-plasma and serum, and the presence of CD41a on theses EVs suggests that they are released from platelets. Furthermore, only a small number of EVs in blood were double positive for CD63 and CD81. The CD63+ EVs were enriched in serum, while CD81+ vesicles were the rarest subpopulation in both plasma and serum. Together, these findings show that multiple subpopulations of EVs are present in blood including CD9+/CD41a+, CD9+/CD63+/CD41+, CD63+/CD41a+, CD63+/CD9+/CD81−, CD81+/CD9+/CD63−, and CD9+/CD63+/CD81+ and that their presence is dissimilar in EDTA-plasma, ACD-plasma and serum.

2022-05-20 | PXD026863 | Pride

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