Long oligonucleotide microarrays for African green monkey gene expression profile analysis

@article{Jacquelin2007LongOM,
  title={Long oligonucleotide microarrays for African green monkey gene expression profile analysis},
  author={B{\'e}atrice Jacquelin and Véronique Mayau and Guillaume Brysbaert and B{\'e}atrice Regnault and O. M. Diop and Fernando Arenzana‐Seisdedos and Lars Rogge and Jean Yves Coppee and Françoise Barré-Sinoussi and Arndt Benecke and Michaela M{\"u}ller-Trutwin},
  journal={The FASEB Journal},
  year={2007},
  volume={21},
  pages={3262 - 3271}
}
Nonhuman primates, including African green monkey (AGM), are important models for bio‐medical research. The information on monkey genomes is still limited and no versatile gene expression screening tool is available. We tested human whole genome microarrays for cross‐species reactivity with AGM transcripts using both long oligonucleotide arrays (60‐mer probes) and short oligonucleotide arrays (25‐mer). Using the long oligonucleotide arrays, we detected 4‐fold more AGM transcripts than with the… 
An Overview of Transcriptome Studies in Non-Human Primates
TLDR
Two major methods for transcriptome analysis are summarized here, cDNA cloning and DNA microarrays, which have technical advantages and disadvantages.
Expression sequence tag library derived from peripheral blood mononuclear cells of the chlorocebus sabaeus
TLDR
The EST library provided here will prove useful in gene annotation efforts for future sequencing of the African Green Monkey genomes and will be an important resource for the comparative analysis of gene expression in clinically relevant nonhuman primate and human research.
Human and Macaque Transcriptomes: A Comparison
The initial deciphering of entire genomes from several mammalian species including human, chimpanzee and macaque has now been accomplished and the massive datasets are publicly available in the form
Comparative sequence and expression analyses of African green monkey (Cercopithecus aethiops) TNPO3 from CV-1 cells
TLDR
It is conclusively demonstrated that AGM-TNPO3 is genetically and physiologically almost identical with that of humans and could be a good candidate for HIV and AGM research as well as an ideal system for a TNPO3 vaccine trial.
Identification of brain transcriptional variation reproduced in peripheral blood: an approach for mapping brain expression traits
TLDR
The approach employed here—utilizing higher quality tissue and more precise dissection of brain regions than is usually possible in humans—may provide a powerful means to investigate variation in gene expression relevant to complex brain related traits, including human neuropsychiatric diseases.
HMGA1-dependent and independent 7SK RNA gene regulatory activity
TLDR
The comparison of the effects of wild-type 7SK RNA on cellular transcriptome dynamics with those induced by the two 7SK L2 mutants as well as the changes in gene expression following inhibition of HMGA1 allow the identification and characterization ofHMGA1- dependent and independent effects of 7SK snRNA.
Severe acute respiratory syndrome-coronavirus infection in aged nonhuman primates is associated with modulated pulmonary and systemic immune responses
TLDR
This study provides unique insight into how several parameters of the systemic and mucosal immune response to SARS-CoV infection are significantly modulated by age.
Innate immune activation in primary HIV-1 infection.
TLDR
Understanding the complexity of how innate responses affect the outcome of HIV-1 infection will help in the development of vaccines that can use innate immunity to enhance viral control with minimal pathogenesis.
Hepatic transcriptome implications for palm fruit juice deterrence of type 2 diabetes mellitus in young male Nile rats
TLDR
The results obtained suggest that the anti-diabetic effects of PFJ may be due to mechanisms other than an increase in insulin secretion.
...
...

References

SHOWING 1-10 OF 77 REFERENCES
Long versus short oligonucleotide microarrays for the study of gene expression in nonhuman primates
Leveraging human genomic information to identify nonhuman primate sequences for expression array development
TLDR
This study demonstrates that human genomic DNA sequence can be leveraged to obtain sequence from the 3' end of NHP orthologs and that this sequence can then be used to generate NHP oligonucleotide microarrays.
Comparison of non-human primate and human whole blood tissue gene expression profiles.
TLDR
Results show that human genechips can be used for expression profiling of NHP samples and provide a foundation for the development of tools for comparing human and NHP gene expression profiles.
Three microarray platforms: an analysis of their concordance in profiling gene expression
TLDR
The results indicate that the long oligon nucleotide platform is highly suitable for expression analysis and compares favorably with the cDNA and short oligonucleotide varieties.
Cross-platform expression profiling demonstrates that SV40 small tumor antigen activates Notch, Hedgehog, and Wnt signaling in human cells
TLDR
Data show that SV40 ST expression alters cell survival pathways to sensitize cells to the killing effect of Hedgehog pathway inhibitors, and shows that cyclopamine had a potent killing effect on cells expressing SV40ST.
Microarray analysis of nonhuman primates: validation of experimental models in neurological disorders
TLDR
It is demonstrated that transcript profiling of NHPs could provide comparative genomic data to validate and better focus experimental animal models of human neurological disorders.
Mining the human genome using microarrays of open reading frames
TLDR
A set of microarrays using probes based on open reading frames (ORFs) in 350 Mb of finished and draft human sequence identifies all genes directly from genomic sequence by querying gene expression.
Identification and utilization of inter-species conserved (ISC) probesets on Affymetrix human GeneChip® platforms for the optimization of the assessment of expression patterns in non human primate (NHP) samples
TLDR
It is feasible to use Affymetrix human GeneChip® platforms to assess the expression profiles of NHP for intra-species studies and appropriate normalization methods could be leveraged to greatly improve interspecies correlations.
...
...