scholarly journals Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

2011 ◽  
Vol 40 (1) ◽  
pp. e3-e3 ◽  
Author(s):  
Martin Kircher ◽  
Susanna Sawyer ◽  
Matthias Meyer
Keyword(s):  
Illumina Platform ◽  
Multiplex Sequencing ◽  
Double Indexing

scholarly journals Gut microbiota markers associated with obesity and overweight in Italian adults

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Vanessa Palmas ◽  
Silvia Pisanu ◽  
Veronica Madau ◽  
Emanuela Casula ◽  
Andrea Deledda ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Smoking Status ◽  
16S Rrna Gene Sequencing ◽  
Normal Weight ◽  
Activity Level ◽  
Rrna Gene ◽  
Illumina Platform ◽  
Obesity And Overweight ◽  
Rrna Gene Sequencing

AbstractIn the present study, we characterized the distinctive signatures of the gut microbiota (GM) from overweight/obese patients (OB), and normal-weight controls (NW), both of Sardinian origin. Fecal bacterial composition of 46 OB patients (BMI = 36.6 ± 6.0; F/M = 40/6) was analyzed and compared to that of 46 NW subjects (BMI = 21.6 ± 2.1; F/M = 41/5), matched for sex, age and smoking status, by using 16S rRNA gene sequencing on MiSeq Illumina platform. The gut microbial community of OB patients exhibited a significant decrease in the relative abundance of several Bacteroidetes taxa (i.e. Flavobacteriaceae, Porphyromonadaceae, Sphingobacteriaceae, Flavobacterium, Rikenella spp., Pedobacter spp., Parabacteroides spp., Bacteroides spp.) when compared to NW; instead, several Firmicutes taxa were significantly increased in the same subjects (Lachnospiraceae, Gemellaceae, Paenibacillaceae, Streptococcaceae, Thermicanaceae, Gemella, Mitsuokella, Streptococcus, Acidaminococcus spp., Eubacterium spp., Ruminococcus spp., Megamonas spp., Streptococcus, Thermicanus, Megasphaera spp. and Veillonella spp.). Correlation analysis indicated that body fatness and waist circumference negatively correlated with Bacteroidetes taxa, while Firmicutes taxa positively correlated with body fat and negatively with muscle mass and/or physical activity level. Furthermore, the relative abundance of several bacterial taxa belonging to Enterobacteriaceae family, known to exhibit endotoxic activity, was increased in the OB group compared to NW. The results extend our knowledge on the GM profiles in Italian OB, identifying novel taxa linking obesity and intestine.

scholarly journals Soil Mycobiome Is Shaped by Vegetation and Microhabitats: A Regional-Scale Study in Southeastern Brazil

2021 ◽  
Vol 7 (8) ◽  
pp. 587
Author(s):  
Danielle Hamae Yamauchi ◽  
Hans Garcia Garces ◽  
Marcus de Melo Teixeira ◽  
Gabriel Fellipe Barros Rodrigues ◽  
Leila Sabrina Ullmann ◽  
...  
Keyword(s):  
Fungal Community ◽  
Vegetation Index ◽  
Normalized Difference Vegetation Index ◽  
Deciduous Forest ◽  
Regional Scale ◽  
Southeastern Brazil ◽  
Transitional Region ◽  
Illumina Platform ◽  
Ecological Processes ◽  
Life On Earth

Soil is the principal habitat and reservoir of fungi that act on ecological processes vital for life on Earth. Understanding soil fungal community structures and the patterns of species distribution is crucial, considering climatic change and the increasing anthropic impacts affecting nature. We evaluated the soil fungal diversity in southeastern Brazil, in a transitional region that harbors patches of distinct biomes and ecoregions. The samples originated from eight habitats, namely: semi-deciduous forest, Brazilian savanna, pasture, coffee and sugarcane plantation, abandoned buildings, owls’ and armadillos’ burrows. Forty-four soil samples collected in two periods were evaluated by metagenomic approaches, focusing on the high-throughput DNA sequencing of the ITS2 rDNA region in the Illumina platform. Normalized difference vegetation index (NDVI) was used for vegetation cover analysis. NDVI values showed a linear relationship with both diversity and richness, reinforcing the importance of a healthy vegetation for the establishment of a diverse and complex fungal community. The owls’ burrows presented a peculiar fungal composition, including high rates of Onygenales, commonly associated with keratinous animal wastes, and Trichosporonales, a group of basidiomycetous yeasts. Levels of organic matter and copper influenced all guild communities analyzed, supporting them as important drivers in shaping the fungal communities’ structures.

scholarly journals Expression Profile of New Marker Genes Involved in Differentiation of Canine Adipose-Derived Stem Cells into Osteoblasts

2021 ◽  
Vol 22 (13) ◽  
pp. 6663
Author(s):  
Maurycy Jankowski ◽  
Mariusz Kaczmarek ◽  
Grzegorz Wąsiatycz ◽  
Claudia Dompe ◽  
Paul Mozdziak ◽  
...  
Keyword(s):  
Stem Cells ◽  
In Vitro Culture ◽  
Osteogenic Differentiation ◽  
Molecular Mechanisms ◽  
Marker Genes ◽  
P Value ◽  
Illumina Platform

Next-generation sequencing (RNAseq) analysis of gene expression changes during the long-term in vitro culture and osteogenic differentiation of ASCs remains to be important, as the analysis provides important clues toward employing stem cells as a therapeutic intervention. In this study, the cells were isolated from adipose tissue obtained during routine surgical procedures and subjected to 14-day in vitro culture and differentiation. The mRNA transcript levels were evaluated using the Illumina platform, resulting in the detection of 19,856 gene transcripts. The most differentially expressed genes (fold change >|2|, adjusted p value < 0.05), between day 1, day 14 and differentiated cell cultures were extracted and subjected to bioinformatical analysis based on the R programming language. The results of this study provide molecular insight into the processes that occur during long-term in vitro culture and osteogenic differentiation of ASCs, allowing the re-evaluation of the roles of some genes in MSC progression towards a range of lineages. The results improve the knowledge of the molecular mechanisms associated with long-term in vitro culture and differentiation of ASCs, as well as providing a point of reference for potential in vivo and clinical studies regarding these cells’ application in regenerative medicine.

Keys for microRNA expression profiling of single rat hypothalamic nuclei and multiplex sequencing strategies

2013 ◽  
Vol 99 (1) ◽  
pp. 72-77 ◽  
Author(s):  
A. Baroin-Tourancheau ◽  
X. Benigni ◽  
C. Benoit ◽  
S. Doubi-Kadmiri ◽  
C. M. Vacher ◽  
...  
Keyword(s):  
Expression Profiling ◽  
Microrna Expression ◽  
Hypothalamic Nuclei ◽  
Multiplex Sequencing

scholarly journals Resolving Differential Diagnostic Problems in von Willebrand Disease, in Fibrinogen Disorders, in Prekallikrein Deficiency and in Hereditary Hemorrhagic Telangiectasia by Next-Generation Sequencing

Life ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 202
Author(s):  
Réka Gindele ◽  
Adrienne Kerényi ◽  
Judit Kállai ◽  
György Pfliegler ◽  
Ágota Schlammadinger ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Hereditary Hemorrhagic Telangiectasia ◽  
Von Willebrand Disease ◽  
Differential Diagnostics ◽  
Bleeding Disorders ◽  
Next Generation ◽  
Illumina Platform ◽  
Clinical Patient ◽  
Von Willebrand ◽  
Generation Sequencing

Diagnosis of rare bleeding disorders is challenging and there are several differential diagnostics issues. Next-generation sequencing (NGS) is a useful tool to overcome these problems. The aim of this study was to demonstrate the usefulness of molecular genetic investigations by summarizing the diagnostic work on cases with certain bleeding disorders. Here we report only those, in whom NGS was indicated due to uncertainty of diagnosis or if genetic confirmation of initial diagnosis was required. Based on clinical and/or laboratory suspicion of von Willebrand disease (vWD, n = 63), hypo-or dysfibrinogenemia (n = 27), hereditary hemorrhagic telangiectasia (HHT, n = 10) and unexplained activated partial thromboplastin time (APTT) prolongation (n = 1), NGS using Illumina platform was performed. Gene panel covered 14 genes (ACVRL1, ENG, MADH4, GDF2, RASA1, F5, F8, FGA, FGB, FGG, KLKB1, ADAMTS13, GP1BA and VWF) selected on the basis of laboratory results. We identified forty-seven mutations, n = 29 (6 novel) in vWD, n = 4 mutations leading to hemophilia A, n = 10 (2 novel) in fibrinogen disorders, n = 2 novel mutations in HHT phenotype and two mutations (1 novel) leading to prekallikrein deficiency. By reporting well-characterized cases using standardized, advanced laboratory methods we add new pieces of data to the continuously developing “bleeding disorders databases”, which are excellent supports for clinical patient management.

Extracellular vesicle-associated miRNAs in ovarian cancer – design of an integrated NGS-based workflow for the identification of blood-based biomarkers for platinum-resistance

2019 ◽  
Vol 57 (7) ◽  
pp. 1053-1062 ◽  
Author(s):  
Jan Dominik Kuhlmann ◽  
Issam Chebouti ◽  
Rainer Kimmig ◽  
Paul Buderath ◽  
Michael Reuter ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Cancer Patients ◽  
Independent Set ◽  
Extracellular Vesicle ◽  
Platinum Resistance ◽  
Diagnostic Purpose ◽  
Illumina Platform ◽  
Platinum Sensitive ◽  
Platinum Resistant ◽  
Next Generation Sequencing Ngs

AbstractBackgroundExtracellular vesicle (EV)-associated microRNAs (miRNAs) have been suggested as promising biomarkers for blood-based cancer diagnosis. However, one of the major limitations for the use of EVs with diagnostic purpose is the lack of standardized EV-profiling techniques. In this regard, the objective of our study was to design an integrated next-generation sequencing (NGS)-based workflow for analyzing the signature of EV-associated miRNA in the plasma of platinum-resistant ovarian cancer patients.MethodsFor EV-extraction, different enrichment methods were compared (ExoQuick vs. exoRNeasy). NGS was performed with the Illumina platform.ResultsWe established an integrated NGS-based workflow, including EV-enrichment with the ExoQuick system, which resulted in an optimal RNA-yield and consistent small RNA libraries. We applied this workflow in a pilot cohort of clinically documented platinum-sensitive (n=15) vs. platinum-resistant (n=15) ovarian cancer patients, resulting in a panel of mature EV-associated miRNAs (including ovarian cancer associated miR-181a, miR-1908, miR-21, miR-486 and miR-223), which were differentially abundant in the plasma of platinum-resistant patients.ConclusionsThis is the first study, analyzing the profile of EV-associated miRNAs in platinum-resistant ovarian cancer patients. We provide rationale to further validate these miRNA candidates in an independent set of patients, in order to characterize their biomarker potential as predictors for platinum-resistance.

scholarly journals Sequencing and de novo assembly of the Asian gypsy moth transcriptome using the Illumina platform

2016 ◽  
Vol 40 (1) ◽  
pp. 160-167 ◽  
Author(s):  
Fan Xiaojun ◽  
Yang Chun ◽  
Liu Jianhong ◽  
Zhang Chang ◽  
Li Yao
Keyword(s):  
Gypsy Moth ◽  
De Novo Assembly ◽  
De Novo ◽  
Illumina Platform ◽  
Asian Gypsy Moth

scholarly journals Analysis on the prokaryotic microbiome in females and embryonic cell cultures of Rhipicephalus sanguineus tropical and temperate lineages from two specific localities in Brazil

2021 ◽  
Vol 30 (3) ◽  
Author(s):  
Mayara de Cassia Luzzi ◽  
Lucas Amoroso Lopes de Carvalho ◽  
Daniel Guariz Pinheiro ◽  
Leidiane Lima-Duarte ◽  
Jaqueline Valéria Camargo ◽  
...  
Keyword(s):  
Cell Cultures ◽  
Rhipicephalus Sanguineus ◽  
Distribution Patterns ◽  
Embryonic Cell ◽  
Tick Cell ◽  
Illumina Platform ◽  
Region Gene ◽  
Host Environment ◽  
Canine Monocytic Ehrlichiosis ◽  
Vertebrate Hosts

Abstract Two lineages of Rhipicephalus sanguineus are known in Brazil: the temperate or southern and the tropical or northern populations. The distribution patterns of both lineages of R. sanguineus have epidemiological implications that can affect vectorial competence concerning Ehrlichia canis, the agent of canine monocytic ehrlichiosis. Intending to identify the microbiomes of both lineages and compare microorganisms in R. sanguineus, we used the 16S rRNA (V4-V5 region) gene-based metataxonomic approach, through NGS sequencing on the MiSeq Illumina platform. We selected specimens of females from the environment and samples of primary embryonic cell cultures, from both lineages, and this was the first study to investigate the prokaryotic microbiome in tick cell cultures. The results showed that many bacterial taxa detected in the samples were typical members of the host environment. A significant diversity of microorganisms in R. sanguineus females and in embryonic cell cultures from both lineages was found, with emphasis on the presence of Coxiella in all samples, albeit in different proportions. The Coxiella species present in the two lineages of ticks may be different and may have co-evolved with them, thus driving different patterns of interactions between ticks and the pathogens that they can harbor or transmit to vertebrate hosts.

scholarly journals Data Analysis of Multiplex Sequencing at SOLiD Platform: A Probabilistic Approach to Characterization and Reliability Increase

2018 ◽  
Vol 08 (01) ◽  
pp. 26-38
Author(s):  
Fábio Manoel França Lobato ◽  
Carlos Diego Damasceno ◽  
Daniela Soares Leite ◽  
Ândrea Kelly Ribeiro-dos-Santos ◽  
Sylvain Darnet ◽  
...  
Keyword(s):  
Data Analysis ◽  
Probabilistic Approach ◽  
Multiplex Sequencing

scholarly journals Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia

2020 ◽  
Author(s):  
Jessica E. Manning ◽  
Jennifer A. Bohl ◽  
Sreyngim Lay ◽  
Sophana Chea ◽  
Ly Sovann ◽  
...  
Keyword(s):  
Disease Outbreaks ◽  
Bioinformatics Pipeline ◽  
Illumina Platform ◽  
Resource Limited ◽  
First Case ◽  
Rapid Production ◽  
Public Health Information ◽  
Pathogen Genome ◽  
Generation Sequencing

AbstractRapid production and publication of pathogen genome sequences during emerging disease outbreaks provide crucial public health information. In resource-limited settings, especially near an outbreak epicenter, conventional deep sequencing or bioinformatics are often challenging. Here we successfully used metagenomic next generation sequencing on an iSeq100 Illumina platform paired with an open-source bioinformatics pipeline to quickly characterize Cambodia’s first case of COVID-2019.

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