Microarrays seq. Medical search. Frequent questions

Since RNA-seq provides a powerful tool for transcriptome-based applications beyond the limitations of microarrays, we sought to systematically evaluate the performance of RNA-seq-based and microarray-based classifiers in this MAQC-III/SEQC study for clinical endpoint prediction using neuroblastoma as a model. (uni-koeln.de)
Characterization of the neuroblastoma transcriptome by RNA-seq reveals that more than 48,000 genes and 200,000 transcripts are being expressed in this malignancy. (uni-koeln.de)
Two biological techniques are used to study the transcriptome, namely DNA microarray, a hybridization-based technique and RNA-seq, a sequence-based approach. (wikipedia.org)
The stallion sperm transcriptome was interrogated by analyzing sperm and testes RNA on a 21,000-element equine whole-genome oligoarray and by RNA-seq. (uaeu.ac.ae)
Three transcriptomic technologies were exploited: RNA-seq, a classical 3'-biased chicken microarray and a high density, "sense target", whole transcriptome chicken microarray, with each recognising 120-150 regulated genes (curated for duplication and incorrect assignment of some microarray probesets). (essex.ac.uk)
Because accomplishing this with RNA-seq comes with such high costs and data complexity, we believe the time is right to focus our expertise on the type of analysi?s tools that interrogate the whole transcriptome with better reproducibility and coverage than the equivalent amount of sequencing. (genomeweb.com)
RNA-seq lets us investigate and discover the transcriptome, the total cellular content of RNAs including mRNA, rRNA and tRNA. (technologynetworks.com)
RNA-seq has been widely used to study the transcriptome. (nih.gov)

Conclusions: We demonstrate that RNA-seq outperforms microarrays in determining the transcriptomic characteristics of cancer, while RNA-seq and microarray-based models perform similarly in clinical endpoint prediction. (uni-koeln.de)
Gene coexpression analysis refers to the en masse discovery of coexpressed genes from a large variety of transcriptomic experiments. (mdpi.com)

Here we analyze 17 published RNA-seq data sets covering a wide range of cell types and perturbations. (nature.com)

RNA-Seq is a widely used technology that allows an efficient genome-wide quantification of gene expressions for, for example, differential expression (DE) analysis. (frontiersin.org)
Whether you are working with microarrays or RNA-Seq differential expression results from Cuffdiff, CodeLinker can give you the insight you are looking for from your datasets. (genecodes.com)
This is true whether you have generated your data using RNA-Seq for differential expression analysis or you have used microarrays. (genecodes.com)

RPE were analyzed using microarray, ChIP-seq, and whole-genome bisulfite sequencing approaches. (nih.gov)

Despite the popularity of RNA-seq, no bioinformatics tool has been developed to leverage this advantage to identify variants associated with aberrant splicing. (nih.gov)

Within the current research, parallel sets of RNA Seq and Affymetrix microarray data were generated on the single HT 29 colon cancer cell line that was handled with and with out five aza deoxy cytidine, a DNA methylation enzyme inhibitor. (vegfr-3inhibitor.com)

Overall, the circRNA arrays are much more an efficient, robust, and accurate technology that outperforms RNA-seq in circRNA profiling (Table 1). (arraystar.com)

Increased comparability between RNA-Seq and microarray data by utilization of gene sets. (uva.nl)

As microarray hybridization signal is relatively unaffected by the presence of other high abundance RNAs, high sensitivity at one transcript per cell can be achieved. (arraystar.com)
We introduce a novel definition of cross-alignment/cross-hybridization to compare qualitatively the ability of high-throughput mRNA sequencing, RNA-Seq, and microarrays to detect tumor and stromal expression from mixed 'pseudo-xenograft' samples vis-à-vis genes and pathways in cross-alignment (RNA-Seq) and cross-hybridization (microarrays). (biomedcentral.com)
Which platform to use with mixed xenograft samples, microarrays or RNA-Seq, appears to be primarily a question of cost and whether the detection and measurement of expression of specific genes of interest are likely to be affected by cross-hybridization or cross-alignment. (biomedcentral.com)
DNA microarray hybridization analysis stands out for its simplicity, comprehensiveness, data consistency, and high throughput. (medscape.com)

At a typical RNA-seq coverage of 30 million reads, less than 5% of the circular RNAs are distributed in the reliable range (Fig. 2B). (arraystar.com)
On the other hand, microarray accuracy is relatively unaffected by the lowered transcript levels (Fig. 2C) [3], which is well suited for circular RNAs. (arraystar.com)

His research interests are broad, but include the statistical and bioinformatic analysis of microarray, DNA sequence and mass spectrometry data from genetics, genomics, proteomics, and metabolomics. (utoronto.ca)

2011) Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling. (arraystar.com)

RNA-seq is the preferred method and has been the dominant transcriptomics technique since the 2010s. (wikipedia.org)
Dual-species transcriptomics or dual-RNA-seq studies use transcriptomics to assess the transcriptional profiles of multiple organisms originating from the same sample [ 15 ]. (biomedcentral.com)

EISA reveals both transcriptional and post-transcriptional contributions to expression changes, increasing the amount of information that can be gained from RNA-seq data sets. (nature.com)
Three recent studies based on RNA-seq provided evidence that intronic reads might correlate with transcriptional activity. (nature.com)
Some of the most popular techniques that use RNA-seq are transcriptional profiling, single nucleotide polymorphism (SNP) identification, 3 RNA editing and differential gene expression analysis. (technologynetworks.com)

Results: We generate gene expression profiles from 498 primary neuroblastomas using both RNA-seq and 44 k microarrays. (uni-koeln.de)
We also find that RNA-seq provides much more detailed information on specific transcript expression patterns in clinico-genetic neuroblastoma subgroups than microarrays. (uni-koeln.de)
Why use microarray over RNA-seq for circular RNA expression profiling? (arraystar.com)
Home Featured Reviews Why Use Microarray Over RNA-seq for Circular RNA Expression Profiling? (arraystar.com)
circular RNA expression profiling by RNA-seq faces major numerical and practical challenges. (arraystar.com)
To assess genomic changes, we quantified mRNA expression using high throughput sequencing technologies (RNA-Seq) in F. grandis populations in the marshes and estuaries impacted by DH oil release. (biomedcentral.com)
According to lead author Weihong Xu, "lower technical variance with the microarrays translated to increased power for detecting low-level expression changes" compared to RNA-seq. (genomeweb.com)
Our technology follows the use of NGS or Sanger sequencing in discovery to take the workflow downstream with the validation performance of catalog or custom expression microarrays," he said. (genomeweb.com)
Background: Previously, using microarrays and mRNA-Sequencing (mRNA-Seq) we found that occupational exposure to a range of benzene levels perturbed gene expression in peripheral blood mononuclear cells. (cdc.gov)
Myocardial mRNA expression of additional genes measured by both RNA-Seq and microarray. (who.int)
Two different studies explored gene-expression profiling by microarray technology as a tool to accurately diagnose Burkitt lymphoma (BL) and differentiate it from DLBCL due to the significant difference in prognosis and treatment approaches for these diseases. (medscape.com)
Similarly, by using host gene microarrays, one can explore host response at the level of gene expression and provide a molecular description of the events that follow infection. (medscape.com)
High-throughput RNA sequencing (RNA-seq) has revolutionized our understanding of gene expression. (cdc.gov)

Evaluation of factors potentially affecting model performances reveals that prediction accuracies are most strongly influenced by the nature of the clinical endpoint, whereas technological platforms (RNA-seq vs. microarrays), RNA-seq data analysis pipelines, and feature levels (gene vs. transcript vs. exon-junction level) do not significantly affect performances of the models. (uni-koeln.de)
Microarray analysis revealed 6,761 transcripts in the sperm, of which 165 were sperm-enriched, and 155 were differentially expressed between the sperm and testes. (uaeu.ac.ae)
After a brief review of the main issues, methods and tools related to the DE analysis of RNA-Seq data, this article focuses on the impact of both the replicate number and library size in such analyses. (frontiersin.org)
Microarray analysis of distinct gene transcription profiles in non-eosinophilic chronic sinusitis with nasal polyps. (southernbiotech.com)

Preceding research comparing parallel RNA Seq with microarray data have reported very good cor relation between the two platforms. (vegfr-3inhibitor.com)
The Stanford researchers this month published a paper comparing the performance of the new array with RNA-seq. (genomeweb.com)
Comparing to microarray, sequencing-based RNA-seq is able to identify splicing variants and single nucleotide variants in one experiment simultaneously. (nih.gov)

Levels of cross-alignment using the RNA-Seq data are comparable for the mouse, 2.2% of mouse CCDS IDs detected in human, and 9.9% of human CCDS IDs detected in mouse. (biomedcentral.com)
The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. (bioconductor.org)

A simulation study was additional con ducted making use of published parallel RNA Seq and microarray datasets, to assess the consistency of different DEG techniques across platforms and their skill in identifying true positives. (vegfr-3inhibitor.com)
but, to varying degrees, two RNA-seq protocols outperformed three of the microarray platforms in most categories. (nih.gov)
Furthermore, 3 platforms (Agilent and two RNA-seq methods) demonstrated over 80% concordance with the gold standard TaqMan assay in terms of fold-change accuracy. (nih.gov)
BASE ships with default raw data types for many different microarray platforms, including Genepix, Agilent and Illumina. (lu.se)

Gene detection in RNA Seq, not like microarray, is simply not depen dent on probe layout, rather it relies on quick nucleotide reads mapping which might attain exceedingly high resolu tion. (vegfr-3inhibitor.com)
Additionally, the RNA Seq gene counts cover a larger dynamic variety than microarray probe hybridiza tion based mostly layout. (vegfr-3inhibitor.com)
The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output. (bioconductor.org)

Next, 70 million raw reads were generated by RNA-seq of which 50% could be aligned with the horse reference genome. (uaeu.ac.ae)
RNA-seq experiments generate reads derived not only from mature RNA transcripts but also from pre-mRNA. (nature.com)
Although RNA-seq mostly generates reads that map to exons, it also captures less abundant intronic sequences 6 . (nature.com)
RNA-seq data uses short reads of mRNA which is free of intronic non-coding DNA. (technologynetworks.com)

Widely used RNA-seq methods start with adapter ligation and cDNA synthesis of biological RNA samples followed by PCR amplification to generate sequencing libraries1. (cdc.gov)

These analyses are in agreement with oligonucleotide-based microarray analyses, and describe only a subset of significant genes with aberrant regulation in the exposed set. (biomedcentral.com)

Our examine surveyed an array of now made use of algorithms Web page 2 of 14 to determine DEGs in parallel for each microarray and RNA Seq data. (vegfr-3inhibitor.com)
We sought to determine which pair of microarray and RNA Seq algorithms would yield the largest overlap in the DEG lists under the very same statistical significance level. (vegfr-3inhibitor.com)

The lack of efficient and quantitative tRNA-seq methods has hindered biological studies of tRNA. (cdc.gov)

Early RNA-seq techniques used Sanger sequencing technology, a technique that although innovative at the time was also low-throughput and costly. (technologynetworks.com)

This application of RNA-Seq to a non-model, wild, and ecologically significant organism is an important evaluation of the technology to quickly assess similar events in the future. (biomedcentral.com)

To systematically compare the power of RNA-seq and microarray-based models in predicting clinical endpoints, we divide the cohort randomly into training and validation sets and develop 360 predictive models on six clinical endpoints of varying predictability. (uni-koeln.de)
Microarrays make applying RNA-seq discoveries in large clinical studies and, ultimately, the clinic a viable option. (genomeweb.com)

In previous comparisons of the differentially expressed gene lists created employing parallel RNA Seq and microarray information, the biological groups that had been studied were frequently rather distinct. (vegfr-3inhibitor.com)

DNA microarrays exploit primary sequence data to measure transcript levels and detect sequence polymorphisms, for every gene, simultaneously. (medscape.com)

We have developed PVAAS, a tool to identify single nucleotide variants that associated with aberrant alternative splicing from RNA-seq data. (nih.gov)

This review focuses on microarray-based approaches for studying transcription response because they hold exceptional promise for the study of infectious disease. (medscape.com)

Our de novo assembly of RNA-Seq data produced a large set of sequences which included many duplicates and fragments. (biomedcentral.com)
RNA-seq (RNA-sequencing) is a technique that can examine the quantity and sequences of RNA in a sample using next-generation sequencing (NGS) . (technologynetworks.com)

On the other hand, microarray tech nology continues to be broadly implemented because of decrease expenditures and wider availability. (vegfr-3inhibitor.com)

Cite this: Using DNA Microarrays to Study Host-Microbe Interactions - Medscape - Sep 01, 2000. (medscape.com)

What are the applications of RNA-seq? (technologynetworks.com)
Microarray-based genotyping applications, although expected to make substantial contributions in this field, are covered only briefly here. (medscape.com)

He also said the firm "needs to do a better job of explaining the utility of our products in this workflow, as well as where RNA-seq's strengths are synergistic with our microarrays and multiplex technologies" like the company's QuantiGene platform. (genomeweb.com)

Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α). (essex.ac.uk)

Their results clearly demonstrated array performance that will drive the use of microarrays in concert with the growth of information" from next-generation sequencing. (genomeweb.com)

to single end RNA Seq information described in similar reviews. (vegfr-3inhibitor.com)

According to Last, Affy's new array fits downstream of discovery projects driven by RNA-seq. (genomeweb.com)

Anatomy8

Organisms8

Diseases18

Chemicals and Drugs57

Analytical, Diagnostic and Therapeutic Techniques and Equipment70

Phenomena and Processes71

Disciplines and Occupations9

Technology, Industry, Agriculture5

Information Science23

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Transcriptome8

Transcriptomic2

Published RNA-seq data1

Differential expression3

Whole-genome1

Bioinformatics1

Affymetrix1

Outperforms1

Comparability1

Hybridization4

RNAs2

Genomics1

Characterization1

Transcriptomics2

Transcriptional3

Expression13

Analysis4

Comparing3

Comparable2

Platforms4

Probe3

Reads4

CDNA1

Analyses1

Algorithms2

Quantitative1

Sanger1

Organism1

Clinical2

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Transcript levels1

Nucleotide1

Focuses1

Sequences2

Broadly1

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