scholarly journals DNA Microarrays in the Undergraduate Microbiology Lab: Experimentation and Handling Large Datasets in as Few as Six Weeks

2007 ◽  
Vol 8 (1) ◽  
pp. 3-12
Author(s):  
David B. Kushner
Keyword(s):  
Data Analysis ◽  
Undergraduate Students ◽  
Dna Microarrays ◽  
Low Cost ◽  
Microarray Experiment ◽  
Genome Wide ◽  
A Genome ◽  
Hands On ◽  
Wet Lab ◽  
Time Required

DNA microarrays have significantly impacted the study of gene expression on a genome-wide level but also have forced a more global consideration of research questions. As such, it has become critical to introduce undergraduate students to genomics approaches to research. A challenge with performing a DNA microarray experiment in the teaching lab is determining the time required for the study and how to handle the voluminous data generated. At an unexpectedly low cost, a 6-week, project-based lab module has been developed that provides 3 weeks for wet lab (hands-on work with the DNA microarrays) and 3 weeks for dry lab (analyzing data, using databases to help with data analysis, and considering the meaning of data within the large dataset). Options exist for extending the number of weeks dedicated to the project, but 6 weeks is sufficient for providing an introduction to both experimental genomics and data analysis. Students indicate that being able to both perform array experiments and thoroughly analyze data enriches their understanding of genomics and the complexity of biological systems.

Genome-wide identification of SSR markers in the Brassica A genome and their utility in breeding

2016 ◽  
Vol 96 (5) ◽  
pp. 808-818 ◽  
Author(s):  
Neil Hobson ◽  
Habibur Rahman
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Low Cost ◽  
Pak Choi ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range ◽  
Genetic Pools ◽  
High Level ◽  
Simple Sequence

Simple sequence repeat (SSR) markers can be applied to genotyping projects at low cost with inexpensive equipment. The objective of this study was to develop SSR markers from the publically-available genome sequence of Brassica rapa and provide the physical position of these markers on the chromosomes for use in breeding and research. To assess the utility of these new markers, a subset of 60 markers were used to genotype 43 accessions of B. rapa. Fifty-five markers from the 10 chromosome scaffolds produced a total of 730 amplicons, which were then used to perform a phylogenetic analysis of the accessions, illustrating their utility in distinguishing between a wide range of germplasm. In agreement with similar studies of genetic diversity, our markers separated accessions into distinct genetic pools including Chinese cabbage, Chinese winter oilseed, European winter oilseed, Canadian spring oilseed, pak-choi, turnip, and yellow sarson. The results further illustrate the presence of a high level of genetic diversity in B. rapa, and demonstrate the potential of these SSR markers for use in breeding and research.

scholarly journals DNA microarrays, a novel approach in studies of chromatin structure.

2004 ◽  
Vol 51 (1) ◽  
pp. 1-8
Author(s):  
Piotr Widłak
Keyword(s):  
Gene Expression ◽  
Dna Microarray ◽  
Chromatin Structure ◽  
Expression Profiling ◽  
Genetic Information ◽  
Dna Microarrays ◽  
Microarray Technology ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale

The DNA microarray technology delivers an experimental tool that allows surveying expression of genetic information on a genome-wide scale at the level of single genes--for the new field termed functional genomics. Gene expression profiling--the primary application of DNA microarrays technology--generates monumental amounts of information concerning the functioning of genes, cells and organisms. However, the expression of genetic information is regulated by a number of factors that cannot be directly targeted by standard gene expression profiling. The genetic material of eukaryotic cells is packed into chromatin which provides the compaction and organization of DNA for replication, repair and recombination processes, and is the major epigenetic factor determining the expression of genetic information. Genomic DNA can be methylated and this modification modulates interactions with proteins which change the functional status of genes. Both chromatin structure and transcriptional activity are affected by the processes of replication, recombination and repair. Modified DNA microarray technology could be applied to genome-wide study of epigenetic factors and processes that modulate the expression of genetic information. Attempts to use DNA microarrays in studies of chromatin packing state, chromatin/DNA-binding protein distribution and DNA methylation pattern on a genome-wide scale are briefly reviewed in this paper.

scholarly journals Time- and cost-efficient high-throughput transcriptomics enabled by Bulk RNA Barcoding and sequencing

2018 ◽  
Author(s):  
Daniel Alpern ◽  
Vincent Gardeux ◽  
Julie Russeil ◽  
Bart Deplancke
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
High Throughput ◽  
Low Cost ◽  
Cdna Libraries ◽  
List Type ◽  
Library Preparation ◽  
Rna Seq ◽  
Genome Wide ◽  
Hands On

ABSTRACTGenome-wide gene expression analyses by RNA sequencing (RNA-seq) have quickly become a standard in molecular biology because of the widespread availability of high throughput sequencing technologies. While powerful, RNA-seq still has several limitations, including the time and cost of library preparation, which makes it difficult to profile many samples simultaneously. To deal with these constraints, the single-cell transcriptomics field has implemented the early multiplexing principle, making the library preparation of hundreds of samples (cells) markedly more affordable. However, the current standard methods for bulk transcriptomics (such as TruSeq Stranded mRNA) remain expensive, and relatively little effort has been invested to develop cheaper, but equally robust methods. Here, we present a novel approach, Bulk RNA Barcoding and sequencing (BRB-seq), that combines the multiplexing-driven cost-effectiveness of a single-cell RNA-seq workflow with the performance of a bulk RNA-seq procedure. BRB-seq produces 3’ enriched cDNA libraries that exhibit similar gene expression quantification to TruSeq and that maintain this quality, also in terms of number of detected differentially expressed genes, even with low quality RNA samples. We show that BRB-seq is about 25 times less expensive than TruSeq, enabling the generation of ready to sequence libraries for up to 192 samples in a day with only 2 hours of hands-on time. We conclude that BRB-seq constitutes a powerful alternative to TruSeq as a standard bulk RNA-seq approach. Moreover, we anticipate that this novel method will eventually replace RT-qPCR-based gene expression screens given its capacity to generate genome-wide transcriptomic data at a cost that is comparable to profiling 4 genes using RT-qPCR.‘SoftwareWe developed a suite of open source tools (BRB-seqTools) to aid with processing BRB-seq data and generating count matrices that are used for further analyses. This suite can perform demultiplexing, generate count/UMI matrices and trim BRB-seq constructs and is freely available at http://github.com/DeplanckeLab/BRB-seqToolsHighlightsRapid (~2h hands on time) and low-cost approach to perform transcriptomics on hundreds of RNA samplesStrand specificity preservedPerformance: number of detected genes is equal to Illumina TruSeq Stranded mRNA at same sequencing depthHigh capacity: low cost allows increasing the number of biological replicatesProduces reliable data even with low quality RNA samples (down to RIN value = 2)Complete user-friendly sequencing data pre-processing and analysis pipeline allowing result acquisition in a day

scholarly journals ChIPdig: a comprehensive user-friendly tool for mining multi-sample ChIP-seq data

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1295 ◽  
Author(s):  
Ruben Esse
Keyword(s):  
Data Analysis ◽  
High Throughput Sequencing ◽  
Enrichment Analysis ◽  
Peak Calling ◽  
Read Mapping ◽  
Sequencing Technologies ◽  
Genome Wide ◽  
Wet Lab ◽  
User Friendly ◽  
Epigenetic Research

In recent years, epigenetic research has enjoyed explosive growth as high-throughput sequencing technologies become more accessible and affordable. However, this advancement has not been matched with similar progress in data analysis capabilities from the perspective of experimental biologists not versed in bioinformatic languages. For instance, chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is at present widely used to identify genomic loci of transcription factor binding and histone modifications. Basic ChIP-seq data analysis, including read mapping and peak calling, can be accomplished through several well-established tools, but more sophisticated analyzes aimed at comparing data derived from different conditions or experimental designs constitute a significant bottleneck. We reason that the implementation of a single comprehensive ChIP-seq analysis pipeline could be beneficial for many experimental (wet lab) researchers who would like to generate genomic data. Here we present ChIPdig, a stand-alone application with adjustable parameters designed to allow researchers to perform several analyzes, namely read mapping to a reference genome, peak calling, annotation of regions based on reference coordinates (e.g. transcription start and termination sites, exons, introns, and 5' and 3' untranslated regions), and generation of heatmaps and metaplots for visualizing coverage. Importantly, ChIPdig accepts multiple ChIP-seq datasets as input, allowing genome-wide differential enrichment analysis in regions of interest to be performed. ChIPdig is written in R and enables access to several existing and highly utilized packages through a simple user interface powered by the Shiny package. Here, we illustrate the utility and user-friendly features of ChIPdig by analyzing H3K36me3 and H3K4me3 ChIP-seq profiles generated by the modENCODE project as an example. ChIPdig offers a comprehensive and user-friendly pipeline for analysis of multiple sets of ChIP-seq data by both experimental and computational researchers. It is open source and available at https://github.com/rmesse/ChIPdig.

I. Global gene expression profiling using DNA microarrays

2002 ◽  
Vol 282 (3) ◽  
pp. G397-G402 ◽  
Author(s):  
Mayi Arcellana-Panlilio ◽  
Stephen M. Robbins
Keyword(s):  
Dna Microarrays ◽  
Genomic Sequence ◽  
Structural Information ◽  
Global Gene Expression ◽  
Factors Affecting ◽  
Genome Wide ◽  
Specific Hybridization ◽  
A Genome ◽  
Global Gene Expression Profiling ◽  
Wide Scale

Having the complete human genomic sequence poses a new challenge: to use genomic structural information to display and analyze biological processes on a genome-wide scale to assign gene function. DNA microarrays are a miniaturized, ordered arrangement of nucleic acid fragments from individual genes located at defined positions on a solid support, enabling the analysis of thousands of genes in parallel by specific hybridization. This review describes technical aspects, discusses relevant applications, and suggests factors affecting the use of this technology and how it fits in the grand scheme of meeting the needs of the postgenomic era.

scholarly journals Results from a Genome-Wide Association Study (GWAS) in Mastocytosis Reveal New Gene Polymorphisms Associated with WHO Subgroups

2020 ◽  
Vol 21 (15) ◽  
pp. 5506 ◽  
Author(s):  
Bogusław Nedoszytko ◽  
Marta Sobalska-Kwapis ◽  
Dominik Strapagiel ◽  
Magdalena Lange ◽  
Aleksandra Górska ◽  
...  
Keyword(s):  
Association Study ◽  
Dna Microarrays ◽  
Genome Wide Association Study ◽  
Systemic Mastocytosis ◽  
Genome Wide Association ◽  
Control Group ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome ◽  
Cutaneous Mastocytosis

Mastocytosis is rare disease in which genetic predisposition is not fully understood. The aim of this study was to analyze associations between mastocytosis and single nucleotide polymorphisms (SNPs) by a genome-wide association study (GWAS) approach. A total of 234 patients were enrolled in our study, including 141 with cutaneous mastocytosis (CM; 78 children and 63 adults) and 93 with systemic mastocytosis (SM, all adults). The control group consisted of 5606 healthy individuals. DNA samples from saliva or blood were genotyped for 551 945 variants using DNA microarrays. The prevalence of certain SNPs was found to vary substantially when comparing patients and healthy controls: rs10838094 of 5OR51Q1 was less frequently detected in CM and SM patients (OR = 0.2071, p = 2.21 × 10−29), rs80138802 in ABCA2 (OR = 5.739, p = 1.98 × 10−28), and rs11845537 in OTX2-AS1 (rs11845537, OR = 6.587, p = 6.16 × 10−17) were more frequently detected in CM in children and adults. Additionally, we found that rs2279343 in CYP2B6 and rs7601511 in RPTN are less prevalent in CM compared to controls. We identified a number of hitherto unknown associations between certain SNPs and CM and/or SM. Whether these associations are clinically relevant concerning diagnosis, prognosis, or prevention remains to be determined in future studies.

scholarly journals ChIPdig: a comprehensive user-friendly tool for mining multi-sample ChIP-seq data

2017 ◽  
Author(s):  
Ruben Esse ◽  
Alla Grishok
Keyword(s):  
Data Analysis ◽  
High Throughput Sequencing ◽  
Enrichment Analysis ◽  
Peak Calling ◽  
Read Mapping ◽  
Sequencing Technologies ◽  
Genome Wide ◽  
Wet Lab ◽  
User Friendly ◽  
Epigenetic Research

AbstractBackgroundIn recent years, epigenetic research has enjoyed explosive growth as high-throughput sequencing technologies become more accessible and affordable. However, this advancement has not been matched with similar progress in data analysis capabilities from the perspective of experimental biologists not versed in bioinformatic languages. For instance, chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is at present widely used to identify genomic loci of transcription factor binding and histone modifications. Basic ChIP-seq data analysis, including read mapping and peak calling, can be accomplished through several well-established tools, but more sophisticated analyzes aimed at comparing data derived from different conditions or experimental designs constitute a significant bottleneck. We reason that the implementation of a single comprehensive ChIP-seq analysis pipeline could be beneficial for many experimental (wet lab) researchers who would like to generate genomic data.ResultsHere we present ChIPdig, a stand-alone application with adjustable parameters designed to allow researchers to perform several analyzes, namely read mapping to a reference genome, peak calling, annotation of regions based on reference coordinates (e.g. transcription start and termination sites, exons, introns, 5′ UTRs and 3′ UTRs), and generation of heatmaps and metaplots for visualizing coverage. Importantly, ChIPdig accepts multiple ChIP-seq datasets as input, allowing genome-wide differential enrichment analysis in regions of interest to be performed. ChIPdig is written in R and enables access to several existing and highly utilized packages through a simple user interface powered by the Shiny package. Here, we illustrate the utility and user-friendly features of ChIPdig by analyzing H3K36me3 and H3K4me3 ChIP-seq profiles generated by the modENCODE project as an example.ConclusionsChIPdig offers a comprehensive and user-friendly pipeline for analysis of multiple sets of ChIP-seq data by both experimental and computational researchers. It is open source and available at https://github.com/rmesse/ChIPdig.

scholarly journals Defining the Stressome of Mycobacterium avium subsp. paratuberculosis In Vitro and in Naturally Infected Cows

2007 ◽  
Vol 189 (21) ◽  
pp. 7877-7886 ◽  
Author(s):  
Chia-wei Wu ◽  
Shelly K. Schmoller ◽  
Sung Jae Shin ◽  
Adel M. Talaat
Keyword(s):  
Mycobacterium Avium ◽  
Dna Microarrays ◽  
High Sensitivity ◽  
The United States ◽  
Enteric Infection ◽  
Genome Wide ◽  
A Genome ◽  
Number Of Genes ◽  
Mycobacterium Avium Subsp Paratuberculosis

ABSTRACT Mycobacterium avium subsp. paratuberculosis causes an enteric infection in cattle, with a great impact on the dairy industry in the United States and worldwide. Characterizing the gene expression profile of M. avium subsp. paratuberculosis exposed to different stress conditions, or shed in cow feces, could improve our understanding of the pathogenesis of M. avium subsp. paratuberculosis. In this report, the stress response of M. avium subsp. paratuberculosis on a genome-wide level (stressome) was defined for the first time using DNA microarrays. Expression data analysis revealed unique gene groups of M. avium subsp. paratuberculosis that were regulated under in vitro stressors while additional groups were regulated in the cow samples. Interestingly, acidic pH induced the regulation of a large number of genes (n = 597), suggesting the high sensitivity of M. avium subsp. paratuberculosis to acidic environments. Generally, responses to heat shock, acidity, and oxidative stress were similar in M. avium subsp. paratuberculosis and Mycobacterium tuberculosis, suggesting common pathways for mycobacterial defense against stressors. Several sigma factors (e.g., sigH and sigE) were differentially coregulated with a large number of genes depending on the type of each stressor. Subsequently, we analyzed the virulence of six M. avium subsp. paratuberculosis mutants with inactivation of differentially regulated genes using a murine model of paratuberculosis. Both bacterial and histopathological examinations indicated the attenuation of all gene mutants, especially those selected based on their expression in the cow samples (e.g., lipN). Overall, the employed approach profiled mycobacterial genetic networks triggered by variable stressors and identified a novel set of putative virulence genes. A similar approach could be applied to analyze other intracellular pathogens.

Take-Home Mechatronics Control Labs: A Low-Cost Personal Solution and Educational Assessment

2013 ◽  
Author(s):  
Brandon Stark ◽  
Zhuo Li ◽  
Brendan Smith ◽  
YangQuan Chen
Keyword(s):  
Control Theory ◽  
Undergraduate Students ◽  
Low Cost ◽  
Integrated Control ◽  
Effective Control ◽  
Laboratory Setup ◽  
Hands On ◽  
Statics And Dynamics ◽  
Industry And Education ◽  
Almost All

Control theory, once described as the “Physics of the 21st Century,” is pervading to almost all subjects of higher learning. However, it is a difficult topic for many students, especially when introduced at the undergraduate lower level. Providing hands-on experience is often a great aid for teaching difficult concepts, but for control theory forcing a hands-on component can distract from the learning if the students are unprepared. An effective control theory laboratory curriculum builds on the foundations of statics and dynamics, circuit theory, signal processing and programming course-work. However, undergraduate students have a limited educational experience and are typically lacking in one or more of those foundations. Coupled with the unfamiliarity of the common equipment found in teaching labs, students often find themselves overwhelmed and struggle with the setups, limiting their exposure to the topic of control theory. Some industry and education companies have introduced extensive control workstations to bring integrated control theory to a teaching laboratory; however these systems are expensive and specialized, limiting their reach and effectiveness. In this paper, a low-cost mechatronics control theory personal laboratory setup with a proposed curriculum is developed for undergraduate students that addresses their uncertain foundation and improves accessibility by introducing portability to maximize the learning outcomes.

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