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SAMPLES (11)

mace:id
Technology # Array version
Species
Organ
Tissue
Physiopathology
Type
Name

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User name	Brice Targat
Email	targat@ihes.fr
Phone / Fax number	+33(0)160926665 / +33(0)160926609
Location	IHES (Systems Epigenomics Group) - 35 route de Chartres - 91440 Bures sur Yvette, France

Scientific description

Nonhuman primates including African Green Monkey (AGM) are important models for biomedical 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, Applied Biosystems-ABI) and short oligonucleotide arrays (25-mer, Affymetrix). Using the long oligonucleotide arrays we detected four times more AGM transcripts than with the short oligonucleotide technology. The number of detected transcripts was comparable to that detected using human RNA, with 87% of the detected genes being shared between both species. The specificity of the signals obtained with the long oligonucleotide arrays was determined by analyzing the transcriptome of concanavalin A activated CD4+ T cells versus non-activated T cells of two monkey species AGM and macaque. For both species, the genes showing the most significant changes in expression, such as IL-2R, were those known to be also regulated in human CD4+ T cell activation. Finally, tissue-specificity of the signals was established by comparing the transcription profiles of AGM brain and tonsil cells. In conclusion, the ABI human microarray platform provides a highly valuable tool for the assessment of AGM gene expression profiles.
Keywords: Defining a microarray platform to study the AGM transcriptome by cross-species and cross-platform comparison

Technical description

5 healthy chinese rhesus macaques and 5 AGM (sabaeus, Senegal) were used in this study. PBMC were isolated from blood samples by Ficoll procedures and activated or not for 48H with concanavaline A. CD4+ cells were then sorted on miltenyi specific column. Total RNA from ConA
activated CD4+ cells from each animal was extracted, pooled to those of the same species and analyzed on both the ABI Human Whole Genome Arrays and Affymetrix U133 Plus 2.0 Arrays with two technical replicates per species. With the Affymetrix array protocol, 4Î¼g of total RNA were used as starting material while 800ng were used with the ABI protocol to generate sufficient hybridization signal. For cross-species comparisons of the ABI platform, total RNA from non activated CD4+ cells isolated from macaques, AGM and human were analyzed. In order to determine optimal quantities of AGM RNA to use on the ABI platform, we tested 4 distinct RNA input quantities (0.5, 0.8, 1.2, and 2Âµg of RNA). We used a pool of total RNA from unstimulated CD4+ T cells isolated from 4 AGM. Tonsil and brain samples were obtained from chronically SIV-infected AGM. Total RNA was analyzed on ABI microarrays.

AGM_stim_1_AB and _2_AB stand for two ABI microarray technical replicates which were hybridized with RNA amplified from 0.8Âµg of AGM total RNA extracted from ConA activated CD4+ T cells as starting material.
AGM_stim_1_Affy and _2_Affy stand for two Affymetrix microarray technical replicates which were hybridized with RNA amplified from 4Âµg of AGM total RNA extracted from ConA activated CD4+ T cells as starting material. 
The ABI microarrays AGM_unstim_1, _2, _3 and _4 were hybridized with RNA amplified from respectively, 0.5, 0.8, 1.2, and 2Âµg of AGM total RNA extracted from unstimulated CD4+ T cells.
MAC_stim_1 and _2 stand for two ABI microarray technical replicates which were hybridized with RNA amplified from 1.2Âµg of macaque total RNA extracted from ConA activated CD4+ T cells. 
MAC_unstim_1 was hybridized with RNA amplified from 1.2Âµg of macaque total RNA extracted from unstimulated CD4+ T cells.
HUM_unstim_1 was hybridized with RNA amplified from 0.8Âµg of human total RNA extracted from unstimulated CD4+ T cells.
The ABI microarrays AGM_tonsil and _brain were hybridized with RNA amplified from 0.8Âµg of AGM total RNA extracted from tonsil and brain tissues, respectively.

References

Jacquelin B, Mayau V, Brysbaert G, Regnault B, Diop OM, Arenzana-Seisdedos F, Rogge L, CoppÃ©e JY, BarrÃ©-Sinoussi F, Benecke A, Muller-Trutwin MC (2007) Long oligonucleotide microarrays for African Green Monkey gene expression profile analysis. FASEB J. 21:3262-71.

Pubmed : http://www.ncbi.nlm.nih.gov/pubmed/17507667

This dataset has previously been published through the GEO database (http://www.ncbi.nlm.nih.gov/geo/) under accession number: GSE6982