Ontology highlight
ABSTRACT:
PROVIDER: PRJNA856490 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
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
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.
2021-06-10 | E-MTAB-10507 | biostudies-arrayexpress
Project description:The use of blood-based extracellular RNA (exRNA) as clinical biomarker requires the implementation of a validated procedure for sample collection, processing and profiling. So far, no study has systematically addressed the pre-analytical variables affecting transcriptome analysis of exRNAs. In the first phase of the exRNAQC study, we evaluated 10 blood collection tubes, 3 time points between blood draw and downstream processing, and 8 RNA purification methods using the supplier-specified minimum and maximum biofluid input volumes. The impact of these pre-analytics is assessed by deep transcriptome profiling of both small and messenger RNA from healthy donors' plasma or serum. In this second phase, we assessed interactions between blood collection tubes, time points and purification methods.
More project info on bioRxiv (manuscript title: Performance of RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control (exRNAQC) study) and https://oncornalab.ugent.be/project/exrnaqc/
| EGAS00001006499 | EGA
Project description:Study to detect possible interactions between blood collection tubes and RNA purification methods on extracellular RNA (exRNA) sequencing. Different combinations of blood collection tubes (3 in total), time intervals between blood draw and downstream processing (immediate (T0), after 4 hours (T4), after 16 hours (T16)), and RNA purification kits (2 in total) were evaluated by applying mRNA capture sequencing (Illumina) to exRNA from human healthy donor plasma or serum.
2022-12-25 | E-MTAB-12541 | biostudies-arrayexpress
Project description:Study to detect possible interactions between blood collection tubes and RNA purification methods on extracellular RNA (exRNA) sequencing. Different combinations of blood collection tubes (3 in total), time intervals between blood draw and downstream processing (immediate (T0), after 4 hours (T4), after 16 hours (T16)), and RNA purification kits (2 in total) were evaluated by applying Small RNA sequencing (Illumina) to exRNA from human healthy donor plasma or serum.
2022-12-25 | E-MTAB-12542 | biostudies-arrayexpress
Project description:The use of blood-based extracellular RNA (exRNA) as clinical biomarker requires the implementation of a validated procedure for sample collection, processing and profiling. So far, no study has systematically addressed the pre-analytical variables affecting transcriptome analysis of exRNAs. In the exRNAQC study, we evaluated 10 blood collection tubes, 3 time points between blood draw and downstream processing, and 8 RNA purification methods using the supplier-specified minimum and maximum biofluid input volumes. The impact of these pre-analytics is assessed by deep transcriptome profiling of both small and messenger RNA from healthy donors' plasma or serum. Experiments are conducted in triplicate (for a total of 276 transcriptomes) using 189 synthetic spike-in RNAs as processing controls. When comparing blood tubes, so-called blood preservation tubes do not stabilize RNA very well, as is reflected by increasing RNA concentration and number of detected genes over time, and by compromised reproducibility. We also document large differences in RNA purification kit performance in terms of sensitivity, reproducibility, and observed transcriptome complexity. Our results are summarized in 11 performance metrics that enable an informed selection of the most optimal sample processing workflow for your own experiments. In conclusion, we put forward robust quality control metrics for exRNA quantification methods with validated standard operating procedures (SOPs) for processing, representing paramount groundwork for future exRNA-based precision medicine applications.
More project info on bioRxiv (manuscript title: Performance of RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control (exRNAQC) study) and https://oncornalab.ugent.be/project/exrnaqc/
| EGAS00001005263 | EGA
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
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.
2015-12-31 | GSE73401 | GEO