scholarly journals Effect of RNA preservation methods on RNA quantity and quality of field collected avian whole blood

2021 ◽  
Author(s):  
Johanna A Harvey ◽  
Sarah A Knutie
Keyword(s):  
Active Material ◽  
Rna Extraction ◽  
Quality Measures ◽  
Rna Degradation ◽  
Blood Samples ◽  
Dry Ice ◽  
Total Rna ◽  
Rna Integrity ◽  
Avian Blood ◽  
Rna Preservation

A limitation of comparative transcriptomic studies of wild avian populations continues to be sample acquisition and preservation to achieve resulting high-quality RNA (i.e., ribonucleic acids that transfers, translates, and regulates the genetic code from DNA into proteins). Field sampling of wild bird samples provides challenges as RNA degradation progresses quickly and because cryopreservation is often not feasible at remote locations. We collected blood samples from songbirds, as avian blood is nucleated and provides sufficient transcriptionally active material in a small and non-lethal sample, to compare the efficacy of widely available RNA stabilizing buffers, RNAlater (Ambion) and DNA/RNA Shield (Zymo) at differing concentrations along with a dry ice-based flash freezing method (Isopropanol 99% and dry ice mixture, -109°C). Each blood sample was divided among five different preservation treatments (dry ice-based flash freezing, RNAlater with 1:5 or 1:10 dilution, or DNA/RNA Shield with 1:2 or 1:3 dilution). A new protocol was optimized for total RNA extraction from avian blood samples with small starting volumes enabling sampling of small passerines. We quantified quality measures, RNA integrity numbers (RINe), rRNA ratios, and total RNA concentrations. We found that RNA preservation buffers, RNAlater and DNA/RNA Shield at all concentrations, provide sample protection from RNA degradation. We suggest caution against using dry ice-based flash-freezing alone for samples preservation as these samples resulted in lower quality measures then samples in preservation buffer. Total RNA concentration was generally not affected by preservation treatment and may vary due to differences in initial samples volumes and carryover across processing steps.

PSXII-4 Impact of delayed processing time on total RNA quality and quantitation of transcript abundance

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 250-250
Author(s):  
Chace Wilson ◽  
Nicholas W Wege Dias ◽  
Stefania Pancini ◽  
Vitor R G Mercadante ◽  
Fernando Biase
Keyword(s):  
Processing Time ◽  
White Blood Cells ◽  
Transcript Abundance ◽  
Rna Degradation ◽  
Biological Information ◽  
Gene Transcript ◽  
Sample Collection ◽  
Blood Samples ◽  
Total Rna ◽  
Rna Integrity

Abstract Critical biological information related to economically important traits is present in the blood transcriptome in cattle. Following a sample collection, however, RNA molecules containing this valuable information are prone to degradation affecting transcript abundance. Thus, proper sample handling and storage is essential when working with RNA. Here, we hypothesized that delayed time between sample collection and processing would lead to RNA degradation and alter gene transcript quantification. We aimed to determine the effect of delayed processing of whole blood on transcriptomic profiles in peripheral white blood cells (PWBC). We collected blood samples (10ml) in tubes containing anticoagulant (K2EDTA) from estrus synchronized beef heifers (n = 5). The tubes remained chilled on ice until processing time. From each heifer, we collected five samples from the jugular vein. We processed one sample from each animal within one hour of collection, and we delayed the processing time of the remaining samples to three, six, eight, and 24 hours post collection. We extracted total RNA from PWBCs, measured yield and assessed quality. We also quantified transcript abundance of 12,724 genes by RNA-sequencing. Samples processed 24 hours post collection had lower RNA integrity number (RIN) compared to samples processed withing one hour of collection (RIN24h=8.00±0.37, RIN1h=8.52±0.37, P = 0.03). There were four and 504 genes with differential transcript abundance (FDR< 0.05) when comparing eight and 24 hours of delayed processing with samples processed within one hour of collection, respectively. Notably, several genes had >1.4-fold greater transcript abundance when samples were stored on ice for eight or 24 hours. Our results indicate that RNA degradation and cellular activity of PWBCs have critical impact on transcript abundance when blood samples are stored for 24 hours under refrigeration. As the development of RNA-based biomarkers gain importance in cattle production systems, timely handling of samples is critical for accurate results.

scholarly journals Optimized protocol for the extraction of RNA and DNA from frozen whole blood sample stored in a single EDTA tube

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hirotaka Yamagata ◽  
Ayumi Kobayashi ◽  
Ryouichi Tsunedomi ◽  
Tomoe Seki ◽  
Masaaki Kobayashi ◽  
...  
Keyword(s):  
Whole Blood ◽  
Ethylenediaminetetraacetic Acid ◽  
Rna Extraction ◽  
Basic Research ◽  
Rna Degradation ◽  
Disodium Salt ◽  
Water Bath ◽  
High Quality ◽  
Blood Samples ◽  
Rna And Dna

AbstractCryopreservation of whole blood is useful for DNA collection, and clinical and basic research. Blood samples in ethylenediaminetetraacetic acid disodium salt (EDTA) tubes stored at − 80 °C are suitable for DNA extraction, but not for high-quality RNA extraction. Herein, a new methodology for high-quality RNA extraction from human blood samples is described. Quickly thawing frozen whole blood on aluminum blocks at room temperature could minimize RNA degradation, and improve RNA yield and quality compared with thawing the samples in a 37 °C water bath. Furthermore, the use of the NucleoSpin RNA kit increased RNA yield by fivefold compared with the PAXgene Blood RNA Kit. Thawing blood samples on aluminum blocks significantly increased the DNA yield by ~ 20% compared with thawing in a 37 °C water bath or on ice. Moreover, by thawing on aluminum blocks and using the NucleoSpin RNA and QIAamp DNA Blood kits, the extraction of RNA and DNA of sufficient quality and quantity was achieved from frozen EDTA whole blood samples that were stored for up to 8.5 years. Thus, extracting RNA from frozen whole blood in EDTA tubes after long-term storage is feasible. These findings may help advance gene expression analysis, as well as biomarker research for various diseases.

scholarly journals A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Michal Kucharski ◽  
Jaishree Tripathi ◽  
Sourav Nayak ◽  
Lei Zhu ◽  
Grennady Wirjanata ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Rna Extraction ◽  
Transcriptome Data ◽  
High Quality ◽  
Diverse Range ◽  
Human Haemoglobin ◽  
Infected Blood ◽  
Blood Samples ◽  
Total Rna

Abstract Background Sequencing technology advancements opened new opportunities to use transcriptomics for studying malaria pathology and epidemiology. Even though in recent years the study of whole parasite transcriptome proved to be essential in understanding parasite biology there is no compiled up-to-date reference protocol for the efficient generation of transcriptome data from growing number of samples. Here, a comprehensive methodology on how to preserve, extract, amplify, and sequence full-length mRNA transcripts from Plasmodium-infected blood samples is presented that can be fully streamlined for high-throughput studies. Results The utility of various commercially available RNA-preserving reagents in a range of storage conditions was evaluated. Similarly, several RNA extraction protocols were compared and the one most suitable method for the extraction of high-quality total RNA from low-parasitaemia and low-volume blood samples was established. Furthermore, the criteria needed to evaluate the quality and integrity of Plasmodium RNA in the presence of human RNA was updated. Optimization of SMART-seq2 amplification method to better suit AT-rich Plasmodium falciparum RNA samples allowed us to generate high-quality transcriptomes from as little as 10 ng of total RNA and a lower parasitaemia limit of 0.05%. Finally, a modified method for depletion of unwanted human haemoglobin transcripts using in vitro CRISPR-Cas9 treatment was designed, thus improving parasite transcriptome coverage in low parasitaemia samples. To prove the functionality of the pipeline for both laboratory and field strains, the highest  2-hour resolution RNA-seq transcriptome for P. falciparum 3D7 intraerythrocytic life cycle available to  date was generated, and the entire protocol was applied to create the largest transcriptome data from Southeast Asian field isolates. Conclusions Overall, the presented methodology is an inclusive pipeline for generation of good quality transcriptomic data from a diverse range of Plasmodium-infected blood samples with varying parasitaemia and RNA inputs. The flexibility of this pipeline to be adapted to robotic handling will facilitate both small and large-scale future transcriptomic studies in the field of malaria.

scholarly journals Factors Influencing Degradation Kinetics of mRNAs And Half-Lives of MicroRNAs, circRNAs, lncRNAs In Blood In Vitro Using Quantitative PCR

2021 ◽  
Author(s):  
Chong Wang ◽  
Hui Liu
Keyword(s):  
Quantitative Pcr ◽  
Room Temperature ◽  
Degradation Kinetics ◽  
Rna Extraction ◽  
Rna Degradation ◽  
Circular Rnas ◽  
Orthogonal Experimental Design ◽  
Messenger Rnas ◽  
Storage Duration ◽  
Blood Samples

Abstract Background: RNAs are rapidly degraded in samples and during collection, processing and testing. In this study, we used the same method to explore the half-lives of different RNAs and the influencing factors, and compared the degradation kinetics and characteristics of different RNAs in whole blood and experimental samples.Methods: Fresh anticoagulant blood samples were incubated at room temperature for different durations, RNAs were extracted, and genes, including internal references, were amplified by real-time quantitative PCR. A linear half-life model was established according to cycle threshold (Ct) values. The effects of experimental operations on RNA degradation before and after RNA extraction were explored. Quantitative analysis of mRNA degradation in samples and during experimental processes were explored using an orthogonal experimental design.Results: The storage duration of blood samples at room temperature had the greatest influence on RNA degradation. The half-lives of messenger RNAs (mRNAs) was 16.4 h. The half-lives of circular RNAs (circRNAs), long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) were 27.6h, 21.1h and 11.4h, respectively.Conclusion: RNA degradation occurred mainly in blood samples, and the half-lives of mRNAs and miRNAs were similar. Quantitative experiments related to mRNAs should be completed within 2 h. The half-lives of circRNAs and lncRNAs were longer than those of the former two.

scholarly journals Acute Effects of Whole Egg Consumption on Circulating MicroRNAs in Sprague Dawley Animals (P15-001-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Amanda Bries ◽  
Joe Webb ◽  
Paige Curry ◽  
Savina Fischer ◽  
Elizabeth McNeill ◽  
...  
Keyword(s):  
Weight Gain ◽  
Corn Oil ◽  
Rna Extraction ◽  
Regulation Of Gene Expression ◽  
Circulating Microrna ◽  
Sprague Dawley ◽  
Total Rna ◽  
Rna Integrity ◽  
Zdf Rats ◽  
Whole Egg

Abstract Objectives MicroRNAs, small ∼22 nt non-coding RNAs, have a functional role in post-transcriptional regulation of gene expression. We have shown that whole egg-based diets reduce weight gain despite increased food intake compared to casein-based diets in Zucker-Diabetic Fatty (ZDF) rats. We hypothesized that the microRNA content of whole egg may underlie the differential impact on weight gain in ZDF rats. Our first objective was to characterize the circulating microRNA content in response to feeding whole egg-based diets over an 8 hour period. Our second objective was to identify and characterize the microRNAs present in whole egg- and casein-based diets. Methods Male Sprague Dawley rats (n = 12; 6 weeks of age) were meal-trained to consume 4 grams of feed in one hour. After one week of meal-training, animals were fasted overnight for 10 hours (h) with water ad libitum followed by controlled feeding of either an AIN93G casein-based diet or isocaloric AIN93G diet containing whole egg (20% egg protein, w/w). At 8 weeks of age, serum was collected via the tail vein at 0, 2, 4, 6, and 8 h following refeeding. Serum microRNA was extracted using a RNA SPLIT kit and prepared for sequencing on an Illumina HiSeq 3000 using a smallRNA Library Prep. Five RNA extraction methods were tested on 6 samples of each diet: 1) Trizol (Invitrogen), 2) Trizol + Directzol (Zymogen), 3) Trizol followed by a second extraction using a fatty acid RNA extraction kit (Norgen), 4) mirPremier (Sigma-Aldrich), 5) ISOLATE II RNA (Bioline). RNA 260/280 ratios were assessed via Nanodrop and RNA integrity was assessed on an Agilent Bioanalyzer. Results The greatest total RNA recovery (ng/µL) and most accurate 260/280 absorbance ratios were achieved using Trizol. The following concentrations of extracted RNA and their respective ratios (means ± SD) were achieved for each dietary component: casein diet (460.9 ± 528.1; 1.56 ± 0.12) and whole egg diet (394.3 ± 292.8; 1.55 ± 0.16), whole egg (73.4 ± 20.3; 1.15 ± 0.23), corn oil (67.5 ± 20.0; 1.41 ± 0.04), and cornstarch (247.12 ± 110.34; 1.64 ± 0.13). Total RNA recovered from the diets had an RNA integrity number (RIN) of 0 and microRNA concentrations were undetected. Conclusions Despite successful total RNA recovery from the diets, all samples had a RIN value of 0, which is not optimal for downstream sequencing. Currently, microRNAs from plasma are being sequenced to determine if varying diets had differential effects on circulating microRNA expression. Funding Sources Presidential Interdisciplinary Research Seed Grant Program, Iowa State University.

scholarly journals A protocol for extraction of total RNA from finger stick whole blood samples preserved with TempusTM solution

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1739 ◽  
Author(s):  
Basirudeen Syed Ahamed Kabeer ◽  
Sara Tomei ◽  
Valentina Mattei ◽  
Tobias Brummaier ◽  
Rose McGready ◽  
...  
Keyword(s):  
Gene Expression ◽  
Whole Blood ◽  
Small Volume ◽  
Rna Extraction ◽  
Cellular Mechanisms ◽  
Blood Samples ◽  
Total Rna ◽  
Low Volume ◽  
Whole Blood Samples ◽  
Finger Stick

Monitoring of blood transcriptional changes during disease or treatment could improve the understanding of cellular mechanisms associated with that particular condition. This can be achieved through serial sampling of small blood volumes. However, molecular analysis of gene expression from low volume samples remains a challenging task. To address this issue, we have developed a set of standard operating procedures (SOP), starting from collection of small volume blood to measurement of gene expression. Previously we published an SOP for the collection of a small volume of blood via finger stick and stabilization of RNA. The aim of this manuscript is to share a modified TempusTM solution based RNA extraction method, developed in our lab, for the extraction of total RNA from low volume whole blood samples collected via finger stick.

scholarly journals A Comprehensive RNA Handling and Transcriptomics Guide for High-Throughput Processing of Plasmodium Blood-Stage Samples.

2020 ◽  
Author(s):  
Michal Kucharski ◽  
Jaishree Tripathi ◽  
Sourav Nayak ◽  
Lei Zhu ◽  
Grennady Wirjanata ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Rna Extraction ◽  
Transcriptome Data ◽  
High Quality ◽  
Diverse Range ◽  
Infected Blood ◽  
Blood Samples ◽  
Total Rna

Abstract BackgroundSequencing technology advancements opened new opportunities to use transcriptomics for studying malaria pathology and epidemiology. Even though in recent years the study of whole parasite transcriptome proved to be essential in understanding parasite biology there is no compiled up-to-date reference protocol for the efficient generation of transcriptome data from growing number of samples. Here, we present a comprehensive methodology on how to preserve, extract, amplify, and sequence full-length mRNA transcripts from Plasmodium-infected blood samples that can be fully streamlined for high-throughput studies.Results We evaluated the utility of various commercially available RNA-preserving reagents in a range of storage conditions. Similarly, we compared several RNA extraction protocols and established the one most suitable for the extraction of high-quality total RNA from low-parasitemia and low-volume blood samples. Furthermore, we updated the criteria needed to evaluate the quality and integrity of Plasmodium RNA in the presence of human RNA. Optimization of SMART-seq2 amplification method to better suit AT-rich P. falciparum RNA samples allowed us to generate high-quality transcriptomes from as little as 10ng of total RNA and a lower parasitemia limit of 0.05%. Finally, we designed a modified method for depletion of unwanted human hemoglobin transcripts using in vitro CRISPR-Cas9 treatment, thus improving parasite transcriptome coverage in low parasitemia samples. To prove the functionality of the pipeline for both laboratory and field strains, we generated the highest 2-hour resolution RNA-seq transcriptome for Plasmodium falciparum 3D7 intraerythrocytic lifecycle available up-to-date and also applied the entire protocol to create the largest transcriptome data from Southeast Asian field isolates.ConclusionsOverall, our methodology presents an inclusive pipeline for generation of good quality transcriptomic data from a diverse range of Plasmodium-infected blood samples with varying parasitemia and RNA inputs. The flexibility of this pipeline to be adapted to robotic handling will facilitate both small and large scale future transcriptomic studies in the field of malaria.

scholarly journals PERBANDINGAN TIGA KIT EKSTRAKSI RNA UNTUK ANALISIS TRANSKRIPTOMIKA PADA KELAPA SAWIT (Elaeis guineensis Jacq.)

2019 ◽  
Vol 6 (1) ◽  
pp. 118
Author(s):  
Siti Zulaeha ◽  
Devit Purwoko ◽  
Imam Cartealy ◽  
Teuku Tajuddin ◽  
. Karyanti ◽  
...  
Keyword(s):  
Somatic Embryo ◽  
Oil Palm ◽  
Elaeis Guineensis ◽  
Early Stage ◽  
Rna Extraction ◽  
Transcriptomic Analysis ◽  
Total Rna ◽  
Rna Integrity ◽  
Rna Quality ◽  
Rna Integrity Number

Comparison of Three RNA Extraction Kits for Transcriptome Analysis of Oil Palm (Elaeis guineensis Jacq.) ABSTRACTObtaining high-quality RNA is very important at an early stage of molecular biology research. To isolate RNA, high skill and caution are required in following laboratory procedures because RNA is easily degraded, especially samples from plant tissue culture. One of the parameters used to check the total RNA quality is RIN (RNA Integrity Number). The aim of this study was to obtain RNA extraction methods on oil palm leaves, callus and somatic embryos that were of good quality and high concentrations for transcriptomic analysis. RNA extraction was carried out using Plant RNA PureLink (Ambion), Genezol RNA Extraction (Geneaid) and RibospinTM Plant (Geneall) kit methods. The results showed that oil palm leaf, callus and somatic embryo RNA were successfully extracted using the RibospinTM (Geneall) kit. Based on the total RNA number of more than 4 μg and the RIN value of more than 7, the extracted RNA could be used in RNA sequencing for transcriptomic analysis. Keywords: callus, oil palm, RNA analysis, RNA quality, somatic embryo ABSTRAKMenghasilkan RNA berkualitas tinggi sangatlah penting pada tahap awal penelitian biologi molekuler. Untuk mengisolasi RNA diperlukan keterampilan dan kehati-hatian tinggi dalam mengikuti prosedur di laboratorium karena RNA lebih mudah terdegradasi, khususnya sampel hasil kultur jaringan tanaman. Salah satu parameter yang digunakan pada pengecekan kualitas RNA total adalah RIN (RNA Integrity Number). Penelitian bertujuan mendapatkan metode ekstraksi RNA pada daun, kalus dan embrio somatik kelapa sawit yang berkualitas baik dan memiliki konsentrasi tinggi untuk analisa transkriptomika.  Ekstraksi RNA dilakukan menggunakan metode kit Plant RNA PureLink (Ambion), Genezol RNA Extraction (Geneaid) dan RibospinTM Plant (Geneall). Hasil menunjukkan bahwa RNA daun, kalus dan embrio somatik kelapa sawit telah berhasil diekstraksi dengan menggunakan kit RibospinTM (Geneall). RNA hasil ekstraksi tersebut dapat digunakan untuk sekuensing RNA dengan tujuan analisis transkriptomika, dilihat dari jumlah total RNA yang lebih dari 4 μg dan nilai RIN lebih dari 7. Kata Kunci: analisis RNA, embrio somatic, kalus, kelapa sawit, kualitas RNA 

scholarly journals A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples

2020 ◽  
Author(s):  
Michal Kucharski ◽  
Jaishree Tripathi ◽  
Sourav Nayak ◽  
Lei Zhu ◽  
Grennady Wirjanata ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Rna Extraction ◽  
Transcriptome Data ◽  
High Quality ◽  
Diverse Range ◽  
Human Haemoglobin ◽  
Infected Blood ◽  
Blood Samples ◽  
Total Rna

Abstract BackgroundSequencing technology advancements opened new opportunities to use transcriptomics for studying malaria pathology and epidemiology. Even though in recent years the study of whole parasite transcriptome proved to be essential in understanding parasite biology there is no compiled up-to-date reference protocol for the efficient generation of transcriptome data from growing number of samples. Here, a comprehensive methodology on how to preserve, extract, amplify, and sequence full-length mRNA transcripts from Plasmodium-infected blood samples is presented that can be fully streamlined for high-throughput studies.ResultsThe utility of various commercially available RNA-preserving reagents in a range of storage conditions was evaluated. Similarly, several RNA extraction protocols were compared and the one most suitable method for the extraction of high-quality total RNA from low-parasitaemia and low-volume blood samples was established. Furthermore, the criteria needed to evaluate the quality and integrity of Plasmodium RNA in the presence of human RNA was updated. Optimization of SMART-seq2 amplification method to better suit AT-rich Plasmodium falciparum RNA samples allowed us to generate high-quality transcriptomes from as little as 10ng of total RNA and a lower parasitaemia limit of 0.05%. Finally, a modified method for depletion of unwanted human haemoglobin transcripts using in vitro CRISPR-Cas9 treatment was designed, thus improving parasite transcriptome coverage in low parasitaemia samples. To prove the functionality of the pipeline for both laboratory and field strains, the highest 2-hour resolution RNA-seq transcriptome for P. falciparum 3D7 intraerythrocytic life cycle available up-to-date was generated and the entire protocol was applied to create the largest transcriptome data from Southeast Asian field isolates.ConclusionsOverall, the presented methodology is an inclusive pipeline for generation of good quality transcriptomic data from a diverse range of Plasmodium-infected blood samples with varying parasitaemia and RNA inputs. The flexibility of this pipeline to be adapted to robotic handling will facilitate both small and large-scale future transcriptomic studies in the field of malaria.

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