scholarly journals A streamlined, cost-effective, and specific method to deplete transcripts for RNA-seq

2020 ◽  
Author(s):  
Amber Baldwin ◽  
Adam R Morris ◽  
Neelanjan Mukherjee
Keyword(s):  
Cost Effective ◽  
Circular Rnas ◽  
Specific Method ◽  
Rna Seq ◽  
Gold Standard Method ◽  
Wide Range ◽  
Rrna Depletion ◽  
Commercial Kits ◽  
The Cost

RNA-sequencing is a powerful and increasingly prevalent method to answer biological questions. Depletion of ribosomal RNA (rRNA), which accounts for 80% of total RNA, is an extremely important step to increase the power of RNA-seq. Selection for polyadenylated RNA is a commonly used approach that excludes rRNA, as well as, important non-polyadenylated RNAs, such as histones, circular RNAs, and many long noncoding RNAs. Commercial methods to deplete rRNA are cost-prohibitive and the gold standard method is no longer available as a standalone kit. Alternative non-commercial methods suffer from inconsistent depletion. Through careful characterization of all reaction parameters, we developed an optimized RNaseH-based depletion of human rRNA. Our method exhibited comparable or better rRNA depletion compared to commercial kits at a fraction of the cost and across a wide-range of input RNA amounts.

Characterization of TiO2 Fabricated by the Cost Effective CBD Method

2021 ◽  
Vol 10 (2) ◽  
pp. 1-4
Author(s):  
Jasmitha Kaza ◽  
Desowja Hanumath Sai Kashyap Kaza ◽  
Mallikarjuna Rao Pasumarthi ◽  
P S Avadhani
Keyword(s):  
Cost Effective ◽  
Cbd Method ◽  
The Cost

scholarly journals Recent Applications of RNA Sequencing in Food and Agriculture

2021 ◽  
Author(s):  
Venkateswara R. Sripathi ◽  
Varsha C. Anche ◽  
Zachary B. Gossett ◽  
Lloyd T. Walker
Keyword(s):  
Rna Sequencing ◽  
Alternative Polyadenylation ◽  
Cost Effective ◽  
Circular Rnas ◽  
Rna Seq ◽  
Complete Collection ◽  
Specific Expression ◽  
Food And Agriculture ◽  
Allele Specific ◽  
Next Generation Sequencing Ngs

RNA sequencing (RNA-Seq) is the leading, routine, high-throughput, and cost-effective next-generation sequencing (NGS) approach for mapping and quantifying transcriptomes, and determining the transcriptional structure. The transcriptome is a complete collection of transcripts found in a cell or tissue or organism at a given time point or specific developmental or environmental or physiological condition. The emergence and evolution of RNA-Seq chemistries have changed the landscape and the pace of transcriptome research in life sciences over a decade. This chapter introduces RNA-Seq and surveys its recent food and agriculture applications, ranging from differential gene expression, variants calling and detection, allele-specific expression, alternative splicing, alternative polyadenylation site usage, microRNA profiling, circular RNAs, single-cell RNA-Seq, metatranscriptomics, and systems biology. A few popular RNA-Seq databases and analysis tools are also presented for each application. We began to witness the broader impacts of RNA-Seq in addressing complex biological questions in food and agriculture.

scholarly journals Identification and characterization of circRNAs in the skin during the wool follicle development of Aohan fine wool sheep

2019 ◽  
Author(s):  
Ranran Zhao ◽  
Nan Liu ◽  
Fuhui Han ◽  
Hegang Li ◽  
Jifeng Liu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Circular Rnas ◽  
Follicle Development ◽  
Rna Seq ◽  
Ampk Signaling ◽  
Wool Follicle ◽  
Solid Foundation ◽  
Sheep Shoulder ◽  
Competitive Endogenous Rna

Abstract Background Aohan fine wool sheep (AFWS) is an early fine wool variety breed cultivated in China. The wool has excellent quality and good textile performance. Investigating the molecular mechanisms that regulate wool growth is important for improving wool quality and yield. Circular RNAs (circRNAs) are non-coding RNAs which are widely expressed and can act as a competitive endogenous RNA (ceRNA) to bind to miRNA. Although circRNA has been studied in many fields, research in sheep wool follicles is limited. To understand the regulation of circRNA in the growth of fine wool sheep, we used RNA-seq to identify circRNAs in sheep shoulder skin at three stages, embryonic day 90 (E90d), embryonic day 120 (E120d), and Birth.Results We identified 8,753circRNAs and found that 1,351 were differentially expressed. We also analyzed the classification and characteristic of the circRNAs in sheep shoulder skin. GO and KEGG were used for source genes of circRNAs, and these were mainly enriched in cellular component organization, regulation of primary metabolic process, tight junctions, and the cGMP-PKG and AMPK signaling pathways. In addition, we predicted interactions between 17 circRNAs and 8 miRNAs using miRanda ( http://www.microrna.org/microrna/home.do ). Based on the significant pathways, we speculate the circ-0005720, circ-0001754, circ-0008036, circ-0004032, circ-0005174, circ-0005519, circ-0007826 may play an important role in regulating wool follicle growth in AFWS. 5 circRNAs were randomly selected to validate the results of the RNA-seq by qRT-PCR.Conclusion Our results provide more information about circRNAs in regulating wool follicle development in AFWS and provide a solid foundation for future experiments.

scholarly journals Rapid high throughput template preparation (rHTTP) method: a novel cost effective method of direct PCR for a wide range of plants

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Prassan Choudhary ◽  
Sudipta Das ◽  
Hillol Chakdar ◽  
Arjun Singh ◽  
Sanjay Kumar Goswami ◽  
...  
Keyword(s):  
Ssr Markers ◽  
High Throughput ◽  
Field Experiments ◽  
Dna Isolation ◽  
Cost Effective ◽  
Direct Pcr ◽  
Rice Varieties ◽  
Plant Materials ◽  
Wide Range ◽  
Commercial Kits

Abstract Background Conventional plant DNA isolation methods are complex, time consuming and require technical expertise. These limitations were overcome using the DNA isolation kits which, however significantly add to the research costs. Hence the present study was aimed to develop a high throughput, rapid and inexpensive method of PCR ready DNA template preparation from plant materials. Methods Concentration of SDS in lysis buffer, amount of starting material, period and temperature for lysis were optimized for obtaining PCR ready templates from plant materials. The method was tested using RAPD and ITS specific primers for different plant species like rice, wheat, mustard, pea, soybean, pigeonpea, tomato, maize, march lilly, bougainvillea, Indian blanket flower, nerium, petunia, purple pirouette petunia, moses-in-the-cradle, golden cane palm, duranta, periwinkle, chrysanthemum and two xerophytes viz. Dipterygium glaucum and Crotaleria burhia. SSR markers RM18398 and RM26108 showed successful amplification in rice varieties Improved Pusa Basmati 1 and KS Dev 12. The effectiveness of the method was tested using fresh as well as 1 year old tissues. The storability of the lysate was also tested. Results In this report, we developed a novel method called rapid high throughput template preparation (rHTTP) method to prepare PCR ready DNA templates. Most striking feature of this technique is that it can be done anywhere where water can be boiled by any means. Using rHTTP method, PCR ready templates can be prepared in just 10 min. Robust and reproducible amplification for all the test plants were recorded with RAPD, plant ITS primers and SSR markers following this method. rHTTP methods works well for both fresh as well as old plant tissues. The lysates had a shelf life of 1 month when stored at 4 °C and 3 days when stored at room temperature. Conclusions rHTTP method has several advantages over the other protocols like ease of execution, no requirement of tissue grinding/liquid nitrogen/hazardous chemicals and above all, equally effective for both fresh and old samples. Using this method, costs per prep comes down ~ 10–50 times as compared to most commercial kits. This method can be used for on-field experiments like molecular diagnostics, varietal identification etc.

scholarly journals Accurate quantification of circular RNAs identifies extensive circular isoform switching events

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Jinyang Zhang ◽  
Shuai Chen ◽  
Jingwen Yang ◽  
Fangqing Zhao
Keyword(s):  
False Discovery Rate ◽  
Differential Expression ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Circular Rnas ◽  
Rna Seq ◽  
Rnase R ◽  
False Discovery ◽  
Rrna Depletion ◽  
Accurate Expression

AbstractDetection and quantification of circular RNAs (circRNAs) face several significant challenges, including high false discovery rate, uneven rRNA depletion and RNase R treatment efficiency, and underestimation of back-spliced junction reads. Here, we propose a novel algorithm, CIRIquant, for accurate circRNA quantification and differential expression analysis. By constructing pseudo-circular reference for re-alignment of RNA-seq reads and employing sophisticated statistical models to correct RNase R treatment biases, CIRIquant can provide more accurate expression values for circRNAs with significantly reduced false discovery rate. We further develop a one-stop differential expression analysis pipeline implementing two independent measures, which helps unveil the regulation of competitive splicing between circRNAs and their linear counterparts. We apply CIRIquant to RNA-seq datasets of hepatocellular carcinoma, and characterize two important groups of linear-circular switching and circular transcript usage switching events, which demonstrate the promising ability to explore extensive transcriptomic changes in liver tumorigenesis.

Light Rail Lite or Cost-Effective Improvements to Bus Service?

2005 ◽  
Vol 1927 (1) ◽  
pp. 22-30 ◽  
Author(s):  
Daniel B. Hess ◽  
Brian D. Taylor ◽  
Allison C. Yoh
Keyword(s):  
High Speed ◽  
Low Cost ◽  
Effective Means ◽  
Cost Effective ◽  
Light Rail ◽  
Rapid Transit ◽  
Service Characteristics ◽  
Wide Range ◽  
Bus Service ◽  
The Cost

Bus rapid transit (BRT) is growing rapidly in popularity because it is viewed widely as an efficient and effective means to improve both transit service and patronage. This paper argues that two distinct views of BRT are emerging: ( a) BRT as a new form of high-speed, rubber-tired, rail-like rapid transit and ( b) BRT as a cost-effective way to upgrade both the quality and image of traditional fixed-route bus service. These two views carry different price tags because the cost of planning, constructing, and operating BRT depends on the complexity of new service features and on rises for BRT that offer service characteristics approaching those of light rail. This study fills a gap in the literature on the costs of BRT by examining in detail component costs–-actual costs for recently implemented services and projected costs for planned new services–-for a sample of BRT systems in North American cities. The study examined BRT costs of 14 planned and recently opened BRT systems to determine how the wide range of BRT service and technology configurations affect costs. The study found that although some of the most successful and popular new BRT systems are high-quality services operating in mixed traffic and implemented at relatively low cost, most BRT projects on the drawing boards are more elaborate, more expensive systems than many currently in service. Most new BRT projects emphasize elaborate LRT-type improvements to lines and stations in one or a few corridors rather than less splashy improvements (such as next-bus monitors, signal preemption, queue-jump lanes, and so forth) affecting more lines and modes in local transit networks. Among the 14 systems examined here, most could be characterized as light rail lite.

Cost-effectiveness of targeting chemotherapy with the 70-gene prognostic signature in early-stage breast cancer (ESBC) patients

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. 6570-6570
Author(s):  
K. B. Tong ◽  
E. Chen ◽  
G. Brink ◽  
R. Bender ◽  
F. de Snoo ◽  
...  
Keyword(s):  
Lymph Node ◽  
Cost Effectiveness ◽  
Adjuvant Chemotherapy ◽  
Cost Effective ◽  
Gene Signature ◽  
Risk Classification ◽  
Node Negative ◽  
Life Years ◽  
Wide Range ◽  
The Cost

6570 Background: The 70-gene microarray test (MammaPrint) has been shown to provide additional prognostic information to clinicopathologic risk assessment for women ESBC; however, the cost-effectiveness of this strategy is not well understood. Methods: The objective of this analysis was to estimate the incremental benefits, costs, and cost-effectiveness of the treatments guided by the 70-gene signature versus Adjuvant! Software (AS) to decide on the use of adjuvant chemotherapy for women ≤61 years with lymph node negative, HER-2 negative ESBC with estrogen receptor (ER) positive or negative disease. A Markov model with a lifetime horizon and three health states (alive without recurrence, death from cancer and death from other causes) was constructed using TreeAge Pro software. Risk classification and patient outcomes data were based on a multi-center 70-gene signature validation study. Efficacy of chemotherapy derived from published meta-analysis of clinical trials. Costs and health utilities were obtained from the literature. Costs and benefits were discounted 3%/year. Results: Compared to AS, the 70-gene signature strategy resulted in 35% of patients being reassigned to a different risk classification and avoided chemotherapy in 9% of patients. In the base case, the 70-gene signature strategy was cost neutral (lifetime costs per patient: $178,811 versus $178,893 for the 70-gene signature and AS strategy). Moreover the 70-gene signature strategy was associated with an increase of 0.13 life years (LYs) and 0.16 quality adjusted life years (QALYs). The model results were sensitive to the cost of 70-gene signature test, cost of adjuvant chemotherapy, and relative risk reduction associated with chemotherapy; however, the 70-gene strategy remained cost-effective across a wide range of assumptions. Conclusions: In this analysis, the 70-gene signature was associated with a reduction in chemotherapy use and an increase in life expectancy. The 70-gene signature appears to be a cost-effective strategy for obtaining additional information to guide the decision to use adjuvant chemotherapy in patients with lymph node negative ESBC. [Table: see text]

A review on Development and Characterization of a Cost-Effective Targeted Quality-Driven Antimalarial Product with an Emphasis on Phytosomes

2021 ◽  
Vol 22 ◽  
Author(s):  
E. Bhargav ◽  
Y. Padmanabha Reddy ◽  
K.B. Koteshwara
Keyword(s):  
Low Income ◽  
Cost Effective ◽  
Low Income Countries ◽  
Development Of Resistance ◽  
Infected Rbcs ◽  
Resistant Strains ◽  
The One ◽  
The Cost ◽  
Neural Network Technology

Abstract : Malaria, a protozoan disease led to numerous deaths and several new million cases raised due to the development of resistance as per the WHO malaria report 2019. This can be overcome by the development of an effective targeted plant-based delivery system through phytosomes that are effective in permeation and bioavailability to treat infected RBCs (parasitic cells). This review article explained the development of targeted Nanophytosomes to overcome resistance, to improve efficacy. This review paper also emphasized various quality-driven developmental approaches in developing an antimalarial product at a reasonable cost. By implementing molecular modeling techniques in development, a significant phytoconstituent with the capability of acting at the target (receptor or enzymes) of the parasite and the one with the capability to overcome drug resistance against resistant strains of parasites can be identified. Absorption Distribution Metabolism Excretion and Toxicity (ADMET) studies information provide a route to the design and formulation of a potent antimalarial agent. Efficient targeted Nanophytosomal formulations can be formulated by functionalizing or conjugating with suitable targets to direct the phytoconstituent to the infected RBCs thereby achieving complete parasitic eradication. Artificial Neural Network technology (ANN), Quality by Design (QbD), molecular dynamics, and simulation studies implementation improves quality and reduces the cost of the product, as these malarial products are much utilized in low-income countries. Hence it can be concluded that targeted developmental quality-driven approaches implementation is essential for effective malarial treatment.

scholarly journals Identification and characterization of circular RNAs in Ganoderma lucidum

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Junjie Shao ◽  
Liqiang Wang ◽  
Xinyue Liu ◽  
Meng Yang ◽  
Haimei Chen ◽  
...  
Keyword(s):  
Ganoderma Lucidum ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Circular Rnas ◽  
Rna Seq ◽  
Polysaccharide Biosynthesis ◽  
Genome Wide ◽  
A Genome ◽  
Positive Correlations

Abstract Circular RNAs (circRNAs) play important roles in animals, plants, and fungi. However, no circRNAs have been reported in Ganoderma lucidum. Here, we carried out a genome-wide identification of the circRNAs in G.lucidum using RNA-Seq data, and analyzed their features. In total, 250 and 2193 circRNAs were identified from strand-specific RNA-seq data generated from the polyA(−) and polyA(−)/RNase R-treated libraries, respectively. Six of 131 (4.58%) predicted circRNAs were experimentally confirmed. Across three developmental stages, 731 exonic circRNAs (back spliced read counts ≥ 5) and their parent genes were further analyzed. CircRNAs were preferred originating from exons with flanking introns, and the lengths of the flanking intron were longer than those of the control introns. A total of 200 circRNAs were differentially expressed across the three developmental stages of G. lucidum. The expression profiles of 119 (16.3%) exonic circRNAs and their parent genes showed significant positive correlations (r ≥ 0.9, q < 0.01), whereas 226 (30.9%) exonic circRNAs and their parent genes exhibited significant negative correlations (r ≤ −0.9, q < 0.01), in which 53 parent genes are potentially involved in the transcriptional regulation, polysaccharide biosynthesis etc. Our results indicated that circRNAs are present in G. lucidum, with potentially important regulatory roles.

scholarly journals Comprehensive analysis of RNA-seq kits for standard, low and ultra-low quantity samples

2019 ◽  
Author(s):  
Marie-Ange Palomares ◽  
Cyril Dalmasso ◽  
Eric Bonnet ◽  
Céline Derbois ◽  
Solène Brohard-Julien ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
Alternative Transcript ◽  
Library Preparation ◽  
Rna Seq ◽  
Reference Tissue ◽  
Gold Standard Method ◽  
Differential Gene ◽  
Commercial Kits ◽  
Whole Transcriptome

ABSTRACTHigh-throughput RNA-sequencing has become the gold standard method for whole-transcriptome gene expression analysis, and is widely used in numerous applications to study cell and tissue transcriptomes. It is also being increasingly used in a number of clinical applications, including expression profiling for diagnostics and alternative transcript detection. However, despite its many advantages, RNA sequencing can be challenging in some situations, for instance in cases of low input amounts or degraded RNA samples. Several protocols have been proposed to overcome these challenges, and many are available as commercial kits. In this study, we comprehensively test three recent commercial technologies for RNA-seq library preparation (TruSeq, SMARTer and SMARTer Ultra-Low) on human reference tissue preparations, using standard (1μg), low (100 and 10 ng) and ultra-low (< 1 ng) input amounts, and for mRNA and total RNA, stranded or unstranded. The results are analyzed using read quality and alignment metrics, gene detection and differential gene expression metrics. Overall, we show that the TruSeq kit performs well with an input amount of 100 ng, while the SMARTer kit shows degraded performance for inputs of 100 and 10 ng, and the SMARTer Ultra-Low kit performs relatively well for input amounts < 1 ng. All the results are discussed in detail, and we provide guidelines for biologists for the selection of a RNA-seq library preparation kit.

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