Variability in, variability out: best practice recommendations to standardize pre-analytical variables in the detection of circulating and tissue microRNAs

2017 ◽  
Vol 55 (5) ◽  
Author(s):  
Jenna Khan ◽  
Joshua A. Lieberman ◽  
Christina M. Lockwood
Keyword(s):  
Best Practice ◽  
Rna Extraction ◽  
Storage Conditions ◽  
Sample Collection ◽  
Ischemic Time ◽  
Cold Ischemic Time ◽  
C Storage ◽  
Tissue Specimens ◽  
And Storage

Abstract:microRNAs (miRNAs) hold promise as biomarkers for a variety of disease processes and for determining cell differentiation. These short RNA species are robust, survive harsh treatment and storage conditions and may be extracted from blood and tissue. Pre-analytical variables are critical confounders in the analysis of miRNAs: we elucidate these and identify best practices for minimizing sample variation in blood and tissue specimens. Pre-analytical variables addressed include patient-intrinsic variation, time and temperature from sample collection to storage or processing, processing methods, contamination by cells and blood components, RNA extraction method, normalization, and storage time/conditions. For circulating miRNAs, hemolysis and blood cell contamination significantly affect profiles; samples should be processed within 2 h of collection; ethylene diamine tetraacetic acid (EDTA) is preferred while heparin should be avoided; samples should be “double spun” or filtered; room temperature or 4 °C storage for up to 24 h is preferred; miRNAs are stable for at least 1 year at –20 °C or –80 °C. For tissue-based analysis, warm ischemic time should be <1 h; cold ischemic time (4 °C) <24 h; common fixative used for all specimens; formalin fix up to 72 h prior to processing; enrich for cells of interest; validate candidate biomarkers with in situ visualization. Most importantly, all specimen types should have standard and common workflows with careful documentation of relevant pre-analytical variables.

Effect of hot air disinfestation treatment in combination with simulated air freight conditions on quality of 'Kensington' mango (Mangifera indica Linn.

1996 ◽  
Vol 36 (6) ◽  
pp. 739 ◽  
Author(s):  
KK Jacobi ◽  
LS Wong ◽  
JE Giles
Keyword(s):  
Surface Temperature ◽  
Fruit Quality ◽  
Mangifera Indica ◽  
Storage Conditions ◽  
Control Treatment ◽  
High Humidity ◽  
C Storage ◽  
Hot Air ◽  
And Storage

The quality of 'Kensington' mangoes (Mangifera indica Linn.) from 2 major Queensland production regions was evaluated following a hot air [HAT, also known as vapour heat (VHT)] disinfestation treatment (46.5�C seed surface temperature held for 10 min under conditions of high humidity) combined with a disease control treatment (55�C water for 5 min) prior to HAT, and storage conditions likely to be encountered during air shipment to Japan (either 10�C for 5 days plus 22�C for 5 days, or 13�C for 5 days plus 22�C for 5 days, or 22�C for 10 days). Final quality was optimum if fruit were treated with HAT alone and stored at 22�C. Fruit injury, in the form of skin browning and lenticel spotting, was particularly severe in HAT plus disease controI fruit stored at 10/22�C. Storage at 10�C combined with heat treatments may be too stressful to fruit physiology, leading to fruit injury and reduced fruit quality at the market destination.

Effects of sample collection and storage conditions on DNA damage in buccal cells from agricultural workers

2011 ◽  
Vol 720 (1-2) ◽  
pp. 8-13 ◽  
Author(s):  
Juan F. Muniz ◽  
Linda A. McCauley ◽  
Victoria Pak ◽  
Michael R. Lasarev ◽  
Glen E. Kisby
Keyword(s):  
Dna Damage ◽  
Storage Conditions ◽  
Agricultural Workers ◽  
Sample Collection ◽  
Buccal Cells ◽  
And Storage

scholarly journals Effects of Temperature on Stability of Blood Homocysteine in Collection Tubes Containing 3-Deazaadenosine

2002 ◽  
Vol 48 (11) ◽  
pp. 2017-2022 ◽  
Author(s):  
Diane M Hill ◽  
Lisa J Johnson ◽  
Paul J Burns ◽  
Angela M Neale ◽  
Denise M Harmening ◽  
...  
Keyword(s):  
Repeated Measures ◽  
Time Course ◽  
Hospital Setting ◽  
Storage Conditions ◽  
Effect Of Temperature ◽  
Sample Collection ◽  
Within Subjects ◽  
Effects Of Temperature ◽  
The Stability ◽  
And Storage

Abstract Background: The accuracy of homocysteine (Hcy) results is currently compromised by the requirement to separate the plasma within 1 h of sample collection. We studied the effect of temperature on the stability of plasma Hcy over a 72-h time course in blood collected into evacuated tubes containing either EDTA alone or both EDTA and 3-deazaadenosine (3DA). Methods: We recruited 100 volunteers, including both diseased and healthy individuals with a range of baseline plasma Hcy values, from two centers. Blood samples were collected into tubes containing EDTA, and EDTA plus 3DA and stored at ambient temperature (20–25 °C) or refrigerated (2–8 °C). Aliquots of blood were centrifuged at various times up to 72 h, the plasma was removed, and Hcy was measured by HPLC. Results: Plasma Hcy measurement covering the sample collection and storage conditions during the whole time course was possible on samples from 59 of those recruited. One-way ANOVA for repeated measures within subjects revealed that only samples that were collected into tubes containing EDTA plus 3DA and stored refrigerated were stable over 72 h (P = 0.2761). Conclusions: A combination of 3DA and storage at 2–8 °C will allow collection of samples for plasma Hcy measurement outside of the hospital setting and wider population screening.

scholarly journals Sample collection/stabilization and DNA/RNA extraction from swab samples for microbiome or metagenome analyses

BioTechniques ◽  
2021 ◽  
Author(s):  
David Navarro ◽  
A González ◽  
A Saiz O y Odriozola
Keyword(s):  
Microbial Communities ◽  
Rna Extraction ◽  
Genetic Material ◽  
New Product ◽  
Storage Medium ◽  
Sample Collection ◽  
Bacterial Composition ◽  
Good Preservation ◽  
Dna And Rna ◽  
And Storage

Good preservation and storage are essential to preserving microorganisms’ genetic material in microbial communities from wide array of sample inputs and accurately represent the bacterial composition for further analysis and applications. The objective is to develop a proper preservation and storage medium to preserve DNA and RNA from those microorganisms. DANAGEN-BIOTED has developed a new product to deal with this problem. Click on the To read the full Application forum, click on the View Article button above and download the PDF.

scholarly journals Delivery of High-Quality Biomarker Assays

2002 ◽  
Vol 18 (2) ◽  
pp. 47-56 ◽  
Author(s):  
Brian N. Swanson
Keyword(s):  
Disease Process ◽  
Clinical Pathology ◽  
Storage Conditions ◽  
Quality Data ◽  
Sample Collection ◽  
High Quality ◽  
Exposure Response ◽  
Specificity And Sensitivity ◽  
Safety Studies ◽  
And Storage

Biomarker measurements now support key decisions throughout the drug development process, from lead optimization to regulatory approvals. They are essential for documenting exposure-response relationships, specificity and potency toward the molecular target, untoward effects, and therapeutic applications. In a broader sense, biomarkers constitute the basis of clinical pathology and laboratory medicine. The utility of biomarkers is limited by their specificity and sensitivity toward the drug or disease process and by their overall variability. Understanding and controlling sources of variability is not only imperative for delivering high-quality assay results, but ultimately for controlling the size and expense of research studies. Variability in biomarker measurements is affected by: biological and environmental factors (e.g., gender, age, posture, diet and biorhythms), sample collection factors (e.g., preservatives, transport and storage conditions, and collection technique), and analytical factors (e.g., purity of reference material, pipetting precision, and antibody specificity). The quality standards for biomarker assays used in support of nonclinical safety studies fall under GLP (FDA) regulations, whereas, those assays used to support human diagnostics and healthcare are established by CLIA (CMS) regulations and accrediting organizations such as the College of American Pathologists. While most research applications of biomarkers are not regulated, biomarker laboratories in all settings are adopting similar laboratory practices in order to deliver high-quality data. Because of the escalation in demand for biomarker measurements, the highly-parallel (multi-plexed) assay platforms that have fueled the rise of genomics will likely evolve into the analytical engines that drive the biomarker laboratories of tomorrow.

scholarly journals scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation

2019 ◽  
Vol 21 (1) ◽  
Author(s):  
E. Madissoon ◽  
A. Wilbrey-Clark ◽  
R. J. Miragaia ◽  
K. Saeb-Parsy ◽  
K. T. Mahbubani ◽  
...  
Keyword(s):  
Single Cell ◽  
Human Cell ◽  
Cell Types ◽  
Quality Data ◽  
Cell Type ◽  
Sample Collection ◽  
High Quality ◽  
Fresh Sample ◽  
Ischemic Time ◽  
Cold Ischemic Time

Abstract Background The Human Cell Atlas is a large international collaborative effort to map all cell types of the human body. Single-cell RNA sequencing can generate high-quality data for the delivery of such an atlas. However, delays between fresh sample collection and processing may lead to poor data and difficulties in experimental design. Results This study assesses the effect of cold storage on fresh healthy spleen, esophagus, and lung from ≥ 5 donors over 72 h. We collect 240,000 high-quality single-cell transcriptomes with detailed cell type annotations and whole genome sequences of donors, enabling future eQTL studies. Our data provide a valuable resource for the study of these 3 organs and will allow cross-organ comparison of cell types. We see little effect of cold ischemic time on cell yield, total number of reads per cell, and other quality control metrics in any of the tissues within the first 24 h. However, we observe a decrease in the proportions of lung T cells at 72 h, higher percentage of mitochondrial reads, and increased contamination by background ambient RNA reads in the 72-h samples in the spleen, which is cell type specific. Conclusions In conclusion, we present robust protocols for tissue preservation for up to 24 h prior to scRNA-seq analysis. This greatly facilitates the logistics of sample collection for Human Cell Atlas or clinical studies since it increases the time frames for sample processing.

scholarly journals Influence of Alcohol Content and Storage Conditions on the Physicochemical Stability of Spirit Drinks

Foods ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1264
Author(s):  
Mateusz Różański ◽  
Katarzyna Pielech-Przybylska ◽  
Maria Balcerek
Keyword(s):  
Volatile Compounds ◽  
Storage Temperature ◽  
Storage Conditions ◽  
Deionized Water ◽  
Higher Alcohols ◽  
Alcohol Content ◽  
C Storage ◽  
Physicochemical Stability ◽  
Different Temperatures ◽  
And Storage

The purpose of this study was to investigate the effects of alcohol by volume (ABV) and storage temperature on changes in the clarity of rye and plum distillates, and their content of volatile compounds. Distillates with initial ABVs of 93.26% v/v (rye distillate) and 82.03% v/v (plum distillate) were diluted with deionized water to 40, 50, and 70% v/v. The samples were stored in darkness at different temperatures (−18 °C, 0 °C, 8 °C, 20 °C) for 8 weeks. The results showed that reducing the alcohol content and storage temperature caused turbidity to increase. The samples prepared from rye distillate were characterized by significantly lower turbidity than those produced from plum distillate. The highest increase in turbidity in comparison to the controls was observed in the samples with 40% v/v alcohol content stored at a temperature of −18 °C. Storage of the rye and plum distillates samples at different temperatures resulted in changes to the concentrations of volatile compounds, i.e., lower levels of acetaldehyde and higher alcohols, and increased content of esters. However, the alcohol content and storage temperature had no statistically significant effect on methanol concentration.

scholarly journals Optimized Fixation and Storage Conditions for FISH Analysis of Single-cell Suspensions

1998 ◽  
Vol 46 (8) ◽  
pp. 971-973 ◽  
Author(s):  
Sarah Murrell-Bussell ◽  
Dianne Nguyen ◽  
Wendy D. Schober ◽  
Jeffrey Scott ◽  
Joe Leigh Simpson ◽  
...  
Keyword(s):  
Storage Conditions ◽  
Fish Analysis ◽  
Flow Cytometric ◽  
Maternal Peripheral Blood ◽  
Flow Cytometric Sorting ◽  
Fish Detection ◽  
And Storage ◽  
Phosphate Buffered Saline

SUMMARY In our protocol to isolate and identify fetal cells in maternal peripheral blood, antibody (Ab)-stained cells are preserved with paraformaldehyde (PF) before batch flow cytometric sorting. However, PF fixation compromises the quality of subsequent interphase fluorescence in situ hybridization (FISH). We therefore examined the effect of PF concentrations and storage time in phosphate-buffered saline (PBS) on the quality of FISH signals. Cells were analyzed for changes in light scatter, morphology, and accessibility of target cell DNA. Fixation in 3% PF for 1 hr was ideal for both flow cytometry and subsequent FISH detection. However, beyond 10 days of storage, FISH quality deteriorated.

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