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Agrigenomics Research Community

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Arrays and RNA-seq in transcriptomics

Validating complex biology: how arrays can complement your next-gen data

Validating complex biology: how arrays can complement your next-gen data

Hosted by Science Magazine, December 2012.
This webinar discusses the challenges of data intensive sequencing studies and the benefit of validation with orthogonal technologies such as microarrays.

RNA-seq and microarray complement each other in transcriptome profiling

RNA-seq and microarray complement each other in transcriptome profiling

Kogenaru S., et al. BMC Genomics 13:629 (2012).
This detailed comparison of array and RNA-Seq concludes that employing multiple transcriptomics methods provides the best picture of the transcriptome.

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling

Labaj P. P., et al. Bioinformatics 27(13):i383-i391 (2011).
This study indicates that RNA-Seq data is dominated by highly expressed transcripts making array technology a better choice for measuring low expressed transcripts.

Quantitative miRNA expression analysis: Comparing microarrays with next-generation sequencing

Quantitative miRNA expression analysis: Comparing microarrays with next-generation sequencing

Willenbrock H., et al. RNA 15(11):2028-2034 (2009).
Comparison of RNA-seq and microarrays in a model system of synthetic RNAs suggests arrays may offer greater accuracy at the expense of de novo discovery.

Learn more about using Affymetrix® Arrays to complement your RNA-seq studies

Learn more about using Affymetrix® Arrays to complement your RNA-seq studies.

Plant transcriptomics

Effects of gibberellin treatment during flowering induction period on global gene expression and the transcription of flowering-control genes in Citrus buds

Effects of gibberellin treatment during flowering induction period on global gene expression and the transcription of flowering-control genes in Citrus buds

Goldberg-Moeller R., et al. Plant Sci. 198:46-57 (2013).
Using Affymetrix® Citrus Array to investigate the effect of GA treatments on global gene expression in the bud and on the expression of key flowering genes

Characterization of a Viral Synergism in the Monocot Brachypodium distachyon Reveals Distinctly Altered Host Molecular Processes Associated with Disease

Characterization of a Viral Synergism in the Monocot Brachypodium distachyon Reveals Distinctly Altered Host Molecular Processes Associated with Disease

Mandadi K. K., Scholthof K. B. Plant Physiol. 160:1432-52 (2012).
Using a custom Brachypodium Tiling array to establish Brachypodium as an alternate host to study PMV- and SPMV-host interactions and viral synergism.

A novel family of γ-gliadin genes are highly regulated by nitrogen supply in developing wheat grain

A novel family of γ-gliadin genes are highly regulated by nitrogen supply in developing wheat grain

Wan Y., et al. J Exp Bot. doi:10.1093/jxb/ers318 (2012).
Using a custom Brachypodium Tiling array to establish Brachypodium as an alternate host to study PMV- and SPMV-host interactions and viral synergism.

Establishment of the Lotus japonicus Gene Expression Atlas (LjGEA) and its use to explore legume seed maturation

Establishment of the Lotus japonicus Gene Expression Atlas (LjGEA) and its use to explore legume seed maturation

Verdier J., et al. The Plant Journal doi:10.1111/tpj.12119 (2013).
A gene expression atlas of Lotus japonicus which provides a "one stop shop" for transcriptomics in this species.

Design of a tobacco exon array with application to investigate the differential cadmium accumulation property in two tobacco varieties

Design of a tobacco exon array with application to investigate the differential cadmium accumulation property in two tobacco varieties

Martin F., et al. BMC Genomics 13:674 (2012).
The difference in leaf Cd accumulation between two specific tobacco cultivars is strongly suggested to be solely dependent on genetic factors.

Transcriptome response analysis of Arabidopsis thaliana to leafminer

Transcriptome response analysis of Arabidopsis thaliana to leafminer

Zhang S., et al. BMC Plant Biol. 12:234 (2012).
Local and systemic responses of A. thaliana to leafminer feeding involve genes related to metabolic processes and stimulus responses.

Differential gene expression in Soybean leaf tissues under drought stress

Differential gene expression in Soybean leaf tissues under drought stress

Le D. T., et al. PLoS ONE 7(11):e49522. doi:10.1371/journal.pone.0049522 (2012).
Identification of drought-responsive candidate genes for in-depth characterization and future development of drought-tolerant soybeans.

Animal transcriptomics

Advancing porcine transcriptomics using a second generation whole transcript array

Advancing porcine transcriptomics using a second generation whole transcript array

Prof. Christopher Tuggle, Iowa State University, USA.
A gene expression atlas of the pig, and characterization of the pig blood transcriptome in response to Salmonella, is enabled by a new array design.

A gene expression atlas of the domestic pig

A gene expression atlas of the domestic pig

Freeman T. C., et al. BMC Biol. 10:90 (2012).
A new porcine Affymetrix expression array was designed in order to provide comprehensive coverage of the known pig transcriptome.

Insights into conceptus elongation in ruminants: Roles of ovarian progesterone and the uterus

Insights into conceptus elongation in ruminants: Roles of ovarian progesterone and the uterus

Prof. Thomas E. Spencer, Washington State University, USA.
Analysis of the endometrial transcriptome using GeneChip® Bovine Genome Arrays reveals important insights in regulation of elongation of the conceptus.

Aberrant placenta gene expression pattern in bovine pregnancies established after transfer of cloned or in vitro produced embryos

Aberrant placenta gene expression pattern in bovine pregnancies established after transfer of cloned or in vitro produced embryos

Salilew-Wondim D., et al. Physiol. Genomics 45:28-46 (2013).
Gene, pathway, and molecular function alterations in bovine placentas derived from pregnancies initiated via different artificial reproductive techniques.

Effects of lactation and pregnancy on metabolic and hormonal responses and expression of selected conceptus and endometrial genes of Holstein dairy cattle

Effects of lactation and pregnancy on metabolic and hormonal responses and expression of selected conceptus and endometrial genes of Holstein dairy cattle

Thompson I. M., et al. J Dairy Sci. 10:5645-56 (2012).
The Affymetrix Bovine Genome Microarray was used to evaluate lactation and pregnancy effects on conceptus and endometrial gene expression.

Learn more about Affymetrix transcriptomics solutions

Integrating arrays and RNA-Seq

Integrating arrays and RNA-Seq

Whole-transcriptome arrays

Whole-transcriptome arrays – gene and transcript isoform expression

3' IVT arrays

3' IVT arrays – measurement of global gene expression from the 3' end

miRNA arrays

miRNA arrays – multi-species designs for gene regulation studies

Quantigene Assays

Quantigene Assays – single target or multiplex assays that work on crude extracts

"For Research Use Only. Not for use in diagnostic procedures."

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Archived Webinars +

Plant Genomics Webinar

Validating Complex Biology Webinar

Translating Genetic Biomarkers to the Clinic Webinar

Clinical Validation of Cancer Biomarker Signatures using Array Technology Webinar

Cancer Genomics Webinar

Circulating Tumor Cells Webinar

Warning! The earliest signals for cancer - miRNA regulation

The Hunt for Missing Heritability