Comprehensive Review of Transcriptomics (RNAs) Workflows from Blood Specimens

Husseini, Abbas Ali; Derakhshandeh, Masoud; Tatlisu, Nevruz Berna

doi:10.1080/15422119.2020.1831537

Cited by 11 publications

(13 citation statements)

References 118 publications

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“…A positive photoresist AZ5214E (Merck, Kenil-worth, NJ) was spun on the wafer for 35 s at 4000 rpm to have 1 μm thickness. (5) The wafer was then soft-baked at 110 • C for 50 s before ultraviolet (UV) exposure. (6) The wafer was exposed to UV light with 20 W/m 2 intensity for 7 s to transfer the IDT patterns from the mask.…”

Section: Device Fabricationmentioning

confidence: 99%

Developing a surface acoustic wave‐induced microfluidic cell lysis device for point‐of‐care DNA amplification

Husseini,

Yazdani,

Ghadiri

et al. 2023

Engineering in Life Sciences

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We developed a microchip device using surface acoustic waves (SAW) and sharp‐edge glass microparticles to rapidly lyse low‐level cell samples. This microchip features a 13‐finger pair interdigital transducer (IDT) with a 30‐degree focused angle, creating high‐intensity acoustic beams converging 6 mm away at a 16 MHz frequency. Cell lysis is achieved through centrifugal forces acting on Candida albicans cells and glass particles within the focal area. To optimize this SAW‐induced streaming, we conducted 42 pilot experiments, varying electrical power, droplet volume, glass particle size, concentration, and lysis time, resulting in optimal conditions: an electrical signal of 2.5 W, a 20 μL sample volume, glass particle size below 10 μm, concentration of 0.2 μg, and a 5‐min lysis period. We successfully amplified DNA target fragments directly from the lysate, demonstrating an efficient microchip‐based cell lysis method. When combined with an isothermal amplification technique, this technology holds promise for rapid point‐of‐care (POC) applications.

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Section: Device Fabricationmentioning

confidence: 99%

Developing a surface acoustic wave‐induced microfluidic cell lysis device for point‐of‐care DNA amplification

Husseini,

Yazdani,

Ghadiri

et al. 2023

Engineering in Life Sciences

Self Cite

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“…Plasma samples are obtained by centrifugation of WB samples with anticoagulants, while serum samples are obtained by centrifugation of WB samples without anticoagulants or with procoagulants (Sotelo-Orozco et al 2021). WB, plasma, and serum samples are commonly used for transcriptomic studies due to their sample availability and convenience of collection under ideal conditions (Qin et al 2016;Mjelle et al 2019;Husseini et al 2022). However, the remaining sediment samples after plasma or serum separation are often discarded or stored for biological resource preservation in real-world scenarios.…”

Section: Introductionmentioning

confidence: 99%

“…Given these concerns, our study aimed to assess the viability of employing either PFB or SFB samples as substitute RNA sources in transcriptomic analysis. Previous research have demonstrated the influence of pre-analytical factors on RNA quality and gene expression (Debey-Pascher et al 2011;Mastrokolias et al 2012;Dvinge et al 2014;Shin et al 2014;Zhao et al 2014;Huang et al 2017;Reust et al 2018;Shen et al 2018;Donohue et al 2019;Gautam et al 2019;He et al 2019b;Harrington et al 2020;Xing et al 2021;Chebbo et al 2022;Husseini et al 2022). However, a comprehensive understanding of the similarities and differences among WB, PFB, and SFB samples in transcriptomic research remains elusive, making it crucial to evaluate their suitability for various applications using reliable metrics.…”

Section: Introductionmentioning

confidence: 99%

Plasma-free samples for transcriptomic analysis: a potential alternative to whole blood samples

Chen

Guo

Wang

et al. 2023

Preprint

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RNA sequencing (RNAseq) technology has become increasingly important in precision medicine and clinical diagnostics and emerged as a powerful tool for identifying protein-coding genes, performing differential gene analysis, and inferring immune cell composition. Human peripheral blood samples are widely used for RNAseq, providing valuable insights into individual biomolecular information. Blood samples can be classified as whole blood (WB), plasma, serum, and remaining sediment samples, including plasma-free blood (PFB) and serum-free blood (SFB) samples. However, the feasibility of using PFB and SFB samples for transcriptome analysis remains unclear. In this study, we aimed to assess the viability of employing PFB or SFB samples as substitute RNA sources in transcriptomic analysis and performed a comparative analysis of WB, PFB, and SFB samples for different applications. Our results revealed that PFB samples exhibit greater similarity to WB samples in terms of protein-coding gene expression patterns, differential expression gene profiling, and immunological characterizations, suggesting that PFB can be a viable alternative for transcriptomic analysis. This contributes to the optimization of blood sample utilization and the advancement of precision medicine research.

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“…Good quality of high-throughput technology-based findings, such as those produced by “omics” approaches, is dependent on high quality samples (Alsagaby 2019b ; Horgan et al 2011 ; Lowe et al 2017 ). Preserved integrity of RNA sample is greatly needed to truly reflect the status of in vivo transcriptome (Husseini et al 2021 ). RNA degradation is a physiological process that is tightly regulated to determine the fate of RNA (Houseley et al 2009 ).…”

Section: Introductionmentioning

confidence: 99%

Investigating the impact of RNA integrity variation on the transcriptome of human leukemic cells

Alsagaby

2022

3 Biotech

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High RNA integrity is essential for good quality of transcriptomics profiling. Nevertheless, in some cases samples with low RNA integrity is the only available material to study. This work was set to investigate the impact of thermal-induced RNA degradation on the transcriptomic profiles of human leukemic cells. DNA microarray-based transcriptomics was conducted on two groups of samples; high RNA integrity samples ( n = 4) and low RNA integrity samples ( n = 5). RNA degradation caused limited but noticeable changes in the transcriptomes. Only 1945 (6.7%) of 29,230 genes showed altered quantitation (fold change ≥ two-fold, p value ≤ 0.03, corrected p value ≤ 0.05). RNA degradation had the most impact on short transcripts and those with short distance between their 5’end and the probe binding position. Overall, the present work identified the genes whose relative quantification is sensitive to RNA degradation. Therefore, altered expression of these genes should be interpreted with caution when studied in low integrity RNA samples. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03223-1.

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Comprehensive Review of Transcriptomics (RNAs) Workflows from Blood Specimens

Cited by 11 publications

References 118 publications

Developing a surface acoustic wave‐induced microfluidic cell lysis device for point‐of‐care DNA amplification

Developing a surface acoustic wave‐induced microfluidic cell lysis device for point‐of‐care DNA amplification

Plasma-free samples for transcriptomic analysis: a potential alternative to whole blood samples

Investigating the impact of RNA integrity variation on the transcriptome of human leukemic cells

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