Effects Of Sample Storage Conditions Research Articles

Comparison of global DNA methylation analysis by whole genome bisulfite sequencing and the Infinium Mouse Methylation BeadChip using fresh and fresh-frozen mouse epidermis

ABSTRACT Until recently, studying the murine methylome was restricted to sequencing-based methods. In this study we compared the global DNA methylation levels of hairless mouse epidermis using the recently released Infinium Mouse Methylation BeadChip from Illumina and whole genome bisulphite sequencing (WGBS). We also studied the effect of sample storage conditions by using fresh and fresh-frozen epidermis. The DNA methylation levels of 123,851 CpG sites covered by both the BeadChip and WGBS were compared. DNA methylation levels obtained with WGBS and the BeadChip were strongly correlated (Pearson correlation r = 0.984). We applied a threshold of 15 reads for the WGBS methylation analysis. Even at a threshold of 10 reads, we observed no substantial difference in DNA methylation levels compared with that obtained with the BeadChip. The DNA methylation levels from the fresh and the fresh-frozen samples were strongly correlated when analysed with both the BeadChip (r = 0.999) and WGBS (r = 0.994). We conclude that the two methods of analysis generally work equally well for studies of DNA methylation of mouse epidermis and find that fresh and fresh-frozen epidermis can generally be used equally well. The choice of method will depend on the specific study’s aims and the available resources in the laboratory.

Effect of delay in processing and storage temperature on diagnosis of SARS-CoV-2 by RTPCR testing

PurposeA large number of new molecular or virology laboratories have been established to increase the testing capacity for SARS-CoV-2. Due to heavy workload, there is delay in testing of samples. In order to avoid the negative effect of delayed testing on RTPCR results guidelines are issued from WHO and CDC to transport samples in cold chain. However, in pandemic situations the recommended guidelines for transport and storage conditions are often compromised. This study was conducted to evaluate the effect of sample storage conditions at different temperatures on the results of RT PCR test. MethodsTotal 275 samples were included in this study, among these 126 samples tested positive and 149 samples tested negative. All samples were aliquoted into two and the aliquotes stored in duplicate at 4 ​°C and room temperature. All aliquots stored at both the temperatures were tested by RTPCR every 24 hours up to 5 days. ResultsDiagnostic accuracy decreased from day1 to day 5 at both the storage temperatures i,e 4 ​°C and room temperature in comparison to the initial day results. Positivity decreased on an average of 9.02% at 4 ​°C and at 9.27% at room temperature per day. Among total 126 positive samples on an average false negative and failure of internal control at 4 ​°C and room temperature was 8.86%, 8.22% and 3.64%, and 4.12%, respectively. All the samples with CT value ​< ​30 remained positive at both temperatures up to 5 days. Few samples with >30 CT value showed variable results i.e. positive, negative or internal control failure from day 1 (2nd day after sample collection) onwards. ConclusionsThere was no significant difference between RT PCR results of samples stored at 4 ​°C and room temperature up to 5 days of collection. However internal control failure was more in samples stored at room temperature. Therefore, samples received without cold chain also may be processed by RTPCR and should not be rejected.

Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes.

ABSTRACTMetagenomics is increasingly used to describe microbial communities in biological specimens. Ideally, the steps involved in the processing of the biological specimens should not change the microbiome composition in a way that it could lead to false interpretations of inferred microbial community composition. Common steps in sample preparation include sample collection, storage, DNA isolation, library preparation, and DNA sequencing. Here, we assess the effect of three library preparation kits and two DNA sequencing platforms. Of the library preparation kits, one involved a PCR step (Nextera), and two were PCR free (NEXTflex and KAPA). We sequenced the libraries on Illumina HiSeq and NextSeq platforms. As example microbiomes, two pig fecal samples and two sewage samples of which aliquots were stored at different storage conditions (immediate processing and storage at −80°C) were assessed. All DNA isolations were performed in duplicate, totaling 80 samples, excluding controls. We found that both library preparation and sequencing platform had systematic effects on the inferred microbial community composition. The different sequencing platforms introduced more variation than library preparation and freezing the samples. The results highlight that all sample processing steps need to be considered when comparing studies. Standardization of sample processing is key to generating comparable data within a study, and comparisons of differently generated data, such as in a meta-analysis, should be performed cautiously.IMPORTANCE Previous research has reported effects of sample storage conditions and DNA isolation procedures on metagenomics-based microbiome composition; however, the effect of library preparation and DNA sequencing in metagenomics has not been thoroughly assessed. Here, we provide evidence that library preparation and sequencing platform introduce systematic biases in the metagenomic-based characterization of microbial communities. These findings suggest that library preparation and sequencing are important parameters to keep consistent when aiming to detect small changes in microbiome community structure. Overall, we recommend that all samples in a microbiome study are processed in the same way to limit unwanted variations that could lead to false conclusions. Furthermore, if we are to obtain a more holistic insight from microbiome data generated around the world, we will need to provide more detailed sample metadata, including information about the different sample processing procedures, together with the DNA sequencing data at the public repositories.

Effect of Sample Storage Conditions on Measurements of Salivary Cotinine Levels.

Information on smoking exposure obtained with self-reports may be inaccurate. Cotinine has a large half-life and its salivary levels correlate well with plasmatic levels. The influence of storage conditions on the validity and precision of salivary cotinine assessments has rarely been evaluated. Here, smokers donated saliva samples, which were sent for immediate analysis, mail posting, storage at 4 °C for 30 or 90 days, or storage at −20 °C for 30 or 90 days. Cotinine levels were determined using enzyme-linked immune-sorbent assay. Agreement of cotinine level measurements was assessed using Bland-Altman analyses. Average age (years), duration of smoking (years) and number of cigarettes smoked (/day) were 55.4 (±SD 9.4), 35.1 (±SD 11.3), and 15.3 (±SD 7.6). The mean immediate cotinine level was 457 ng/mL (range 11.3 to 1318 ng/mL). Mean cotinine levels in samples analyzed after delay ranged between 433 ng/mL (−20 °C 30 days) and 468 ng/mL (4 °C 30 days). A dose-response gradient was observed in the relationship between salivary cotinine level and self-reported smoking status. A good agreement between cotinine levels for all storage conditions compared with immediate analysis was observed, with average differences ranging from −11 to 24 ng/mL. Cotinine levels remained stable regardless of the tested condition. The stability of salivary cotinine may enable samples to be obtained in difficult-to-reach areas, reduce study costs, and improve the validity of the information on exposure to smoking.

Storage media and not extraction method has the biggest impact on recovery of bacteria from the oral microbiome

Next Generation sequencing has greatly progressed the exploration of the oral microbiome’s role in dental diseases, however, there has been little focus on the effect of sample storage conditions and their interaction with DNA extraction method. Dental plaque samples collected from 20 healthy participants were pooled and stored in either 75% ethanol or Bead solution for up to 6-months at −80 °C, prior to DNA extraction with either QIAamp (non-bead beating) or PowerSoil (bead-beating) kit, followed by Illumina sequencing of 16S rRNA gene. We found that storage media and not extraction method had the biggest influence on the diversity and abundance of the oral microbiota recovered. Samples stored in Bead solution, independent of the extraction kit, retrieved higher diversity (PowerSoil p = 1.64E-07, QIAamp p = 0.0085) and had dissimilar overall ecologies as indicated by lower level of shared diversity (PowerSoil p = 0.0000237, QIAamp p = 0.0088). Comparatively, samples stored in Bead solution and extracted with PowerSoil recovered a higher abundance of Streptococcus species. These data indicate that Bead solution can preserve the oral microbiome in dental plaque reliably, for periods of up to 6-months at −80 °C, and is compatible, with either a bead-beating or non-bead beating DNA extraction method.

Bladder Cancer Cell Capture: Elucidating the Effect of Sample Storage Conditions on Capturing Bladder Cancer Cells via Surface Immobilized EpCAM Antibody.

The gold standard to detect bladder cancer, cystoscopy, is an invasive procedure requiring ambulant hospitalization, thus presenting an obstacle for routine diagnosis. We aim to develop a noninvasive detection method as an alternative that selectively captures shed cancer cells in the patient's urine via surface-immobilized anti-EpCAM antibody. However, the urine sample storage conditions prior to analysis affect the subsequent cancer cell capture rates by the device. In this study, we investigate the capture rates of HT1197 and HT1376 bladder cancer cells in different media (fresh and aged urine as well as PBS) and storage temperatures prior to analysis (37 and 4 °C) as well as in the presence of adjuvants in the medias (free antibodies and cell debris). Capture efficiencies decreased in as little as 1 h of the sample being incubated at 37 °C in all media studied here. Furthermore, cell debris played a strong part in reducing the capture efficiency. From the data, we conclude that storing the sample at 4 °C resulted in the best capture efficiency if storage of more than 1 h was required, which gave valuable insights for this sensor's translation from laboratory to real-world applications.

The Effects of Sample Storage Conditions on the Microbial Community Composition in Hydraulic Fracturing Produced Water

The petroleum industry has an increasing interest in understanding the microbial communities driving biofouling and biocorrosion in reservoirs, wells, and infrastructure. However, sampling of the relevant produced fluids from subsurface environments for microbiological analyses is often challenged by high liquid pressures, workplace regulations, operator liability concerns, and remote sampling locations. These challenges result in infrequent sampling opportunities and the need to store and preserve the collected samples for several days or weeks. Maintaining a representative microbial community structure from produced fluid samples throughout storage and handling is essential for accurate results of downstream microbial analyses. Currently, no sample handling or storage recommendations exist for microbiological analyses of produced fluid samples. We used 16S rRNA gene sequencing to monitor the changes in microbial communities in hypersaline produced water stored at room temperature or at 4 °C for up to 7 days. We also analyzed storage at −80 °C across a 3-week period. The results suggest ideal handling methods would include placing the collected sample on ice as soon as possible, but at least within 24 h, followed by shipping the samples on ice over 2–3 days, and finally, long-term storage in the −20 °C or −80 °C freezer.

Analytical validation of a quantitative reverse transcriptase polymerase chain reaction assay for evaluation of T-cell targeted immunosuppressive therapy in the dog

Cyclosporine is an immunosuppressive agent that inhibits T-cell function by decreasing production of cytokines such as interleukin-2 (IL-2) and interferon-γ (IFN-γ). In dogs, there is currently no reliable analytical method for determining effective cyclosporine dosages in individual patients. Our laboratory has developed a quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) assay that measures IL-2 and IFN-γ gene expression, with the goal of quantifying immunosuppression in dogs treated with cyclosporine. This study focuses on analytical validation of our assay, and on the effects of sample storage conditions on cyclosporine-exposed samples. Heparinized whole blood collected from healthy adult dogs was exposed to a typical post-treatment blood concentration for cyclosporine (500ng/mL) for 1h, and then stored for 0, 24, and 48h at both room temperature and 4°C. The study was then repeated using a cyclosporine concentration of 75ng/mL, with sample storage for 0, 24, and 48h at 4°C. Cytokine gene expression was measured using RT-qPCR, and assay efficiency and inter- and intra-assay variability were determined. Storage for up to 24h at room temperature, and up to 48h at 4°C, did not significantly alter results compared to samples that were processed immediately. Validation studies showed our assay to be highly efficient and reproducible and robust enough to be feasible under standard practice submission conditions.

Effect of Sample Storage Conditions on Culture-Independent Bacterial Community Measures in Cystic Fibrosis Sputum Specimens

Culture-independent approaches to studying the microbiota of the airways of cystic fibrosis (CF) patients have employed analysis of the bacterial 16S rRNA gene through Sanger sequencing of clone libraries ([5][1], [6][2], [12][3]), terminal restriction fragment length polymorphism analysis ([8][4

Effects of Sample Storage Conditions on Glycated Hemoglobin Measurement: Evaluation of Five Different High Performance Liquid Chromatography Methods

Glycated hemoglobin, reported as hemoglobin A1c (HbA1c), is widely used as a measure of long-term glycemic control in patients with diabetes. The accuracy of measurements depends in part on proper storage of the sample prior to analysis. Three whole blood (WB) samples at three HbA1c levels were collected and stored at -70 degrees C, -20 degrees C, 4 degrees C, room temperature (17-23 degrees C), and 37 degrees C. One aliquot from each temperature was analyzed by each method on days 1, 2, 3, 6, 7, 10, 14, 21, 28, and 57. The Primus CLC (385 and 330) (Primus Corp., Kansas City, MO) showed stability of WB at -20 degrees C and 4 degrees C for 57 days, room temperature for 14 days, and 37 degrees C for 1 day. The Tosoh 2.2 Plus (Tosoh Bioscience, Inc., South San Francisco, CA) showed stability at -20 degrees C for 3 days, 4 degrees C for 14 days, room temperature for 3 days, and 37 degrees C for less than 24 h. With the Tosoh G7, results were acceptable at -20 degrees C for 10 days, 4 degrees C for 57 days, room temperature for 7 days, and 37 degrees C for less than 24 h. The Bio-Rad Variant (Bio-Rad Laboratories, Hercules, CA) showed stability at -20 degrees C for 6 days, 4 degrees C for 14 days, room temperature for 3 days, and 37 degrees C for less than 24 h. The Bio-Rad Variant II showed stability at -20 degrees C for 28 days, 4 degrees C for 57 days, room temperature for 7 days, and 37 degrees C for less than 24 h. All methods either met or exceeded manufacturers' claims for stability. The CLC 385/330, Tosoh G7, and Bio-Rad Variant II high performance liquid chromatography methods showed better stability than the Tosoh 2.2 Plus and Bio-Rad Variant.

Effect of Sample Storage Conditions on Virus Inactivation by Solvent/Detergent

Effect of Sample Storage Conditions on Virus Inactivation by Solvent/Detergent

Diurnal Variability and in Vitro Stability of Carbohydrate-deficient Transferrin

Transferrin isoforms with pI values ≥5.7, known as carbohydrate-deficient transferrin (CDT), are present in increased concentrations in the serum of patients with current alcohol abuse. CDT has been found to be a specific and sensitive marker for detection and monitoring of high and continual alcohol consumption (1). The clinical performance of CDT has been studied using various techniques for analysis but also using various conditions for serum sample collection and sample storage. The biological (non-alcohol-influenced) variation over time has been found to be low (2). We have studied the diurnal variability of CDT and the effect of sample storage conditions in the commercial CDTect assays. Blood was collected by venipuncture and allowed to clot at room temperature. The serum samples were separated by centrifugation, and 1-mL portions were aliquoted into polypropylene tubes (Sarstedt). CDT was measured by duplicate determinations in CDTect® RIA or CDTect EIA (Pharmacia & Upjohn Diagnostics AB). Results are expressed as units per liter. In an evaluation performed on 76 serum samples …

Effect of Sample Storage Conditions on Body Burden Analysis of Organic Contaminants in Unionid Mussels

Abstract In order to quantitatively assess the effect of sample storage conditions on the body burden analysis of organic contaminants, a comparative analysis was carried out on the unionid mussel Elliptic complanata. The mussels were divided into two groups, each with distinct storage conditions, while Group A was kept in the freezer at −20°C, Group B was kept in the refrigerator for five days at 5°C. All the compounds present in the control were also present in Group B samples. Analysis of the organic contaminants in each of these two groups showed that for total PCB concentrations, the two treatments were not significantly different; however when compared individually 6 of the 13 PCB congeners showed significant differences. The observed differences were relatively small for individual PCB congeners (7.1 to 15.3%), higher for chlorobenzenes (10.5 to 36.4%), and yet higher for HCE (44.1%); the difference for HCE, although large is nevertheless not significant, even if only marginally so.