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SAMPLES (11)
mace:id
Technology # Array version
# SEVERAL # # SEVERAL
Affymetrix # HGU 133 Plus 2
Affymetrix # MGU 74 Av2
Affymetrix # MoGene V1.0st
Affymetrix # Mouse 430A
Affymetrix # Rhesus
Agilent # AGHUMAN
Agilent # AGMOUSE
Applied Biosystems # HGS V1
Applied Biosystems # HGS V2
Applied Biosystems # MGS V1
Applied Biosystems # MGS V2
Applied Biosystems # RGS V1
Genopole SXB # SXBH1
Genopole SXB # SXBH2
Genopole SXB # SXBH3
Genopole SXB # SXBM1
Genopole SXB # SXBM2
Genopole SXB # SXBM3
Illumina # HumanHT-12 V4.0
Illumina # HUMANWG6v3
Illumina # MouseWG-6 v2.0
Species
# SEVERAL
Cercocebus atys
Chlorocebus sabaeus
Homo sapiens
Macaca mulatta
Macaca Nemestrina
Mus musculus
Pan troglodytes
Rattus norvegicus
Organ
# OTHER
# SEVERAL
Adenoid
Adrenal gland
Bladder
Blood
Blood vessel
Brain
Bronchi
Cervix
Embryo
Esophagus
Gallblader
Heart
Hypotalamus
Intestine
Kidney
Larynx
Liver
Lung
Lymph node
Mammary gland
Mussle
Pancreas
Parathyroid
Penis
Pharynx
Pineal gland
Pituitary gland
Prostate
Salivary gland
Seminal vesicle
Skin
Spinal cord
Spleen
Stomach
Test
Thymus
Thyroid
Tonsil
Trachea
Ureter
Uterus
Vagina
Vas deferens
Tissue
# OTHER
# SEVERAL
Bone Marrow
Connective - Dense Irregular Tissue (Collagen)
Connective - Dense Regular Tissue (Collagen)
Connective - Dense Regular Tissue (Elastic)
Connective - Loose Tissue (Adipose)
Connective - Loose Tissue (Areolar)
Connective - Loose Tissue (Reticular)
Epithelium - Simple (Columnar)
Epithelium - Simple (Cuboidal)
Epithelium - Simple (Pseudostratified)
Epithelium - Simple (Squamous)
Epithelium - Stratified (Columnar / Cuboidal)
Epithelium - Stratified (Squamous: Keratinized)
Epithelium - Stratified (Squamous: NonKeratinized)
Fluid - Blood
Fluid - Lymph
Gland - Endocrine Glands
Gland - Exocrine Glands (Ducts and Tubules)
Muscle - Non-striated
Muscle - Striated (Cardiac)
Muscle - Striated (Skeletal)
Nervous - Nerves
Nervous - Neurons (Bipolar)
Nervous - Neurons (Multipolar)
Nervous - Neurons (Unipolar)
Nervous - Receptors
Placenta
Stem cells
Supportive - Cartilage (Elastic)
Supportive - Cartilage (Fibrocartilage)
Supportive - Cartilage (Hyaline)
Supportive - Osseous (Compact)
Supportive - Osseous (Spongey)
Physiopathology
# HEALTHY
# OTHER
# SEVERAL
apoptosis
autocrine signaling
differentiation
drug response
electric response
endocrine signaling
environemental response
homeostasis
immune response
mechanic response
necrosis
paracrine signaling
proliferation
Type
# OTHER
# SEVERAL
conditional knockout
drug stress
electric stress
environmental stress
ground state
immune stress
knockdown RNAi
knockout
mechanic stress
stable transfection
time course
transient transfection
Name
Attached file
download project data file ('.map')
Attached file (see:
ruid website
)
download project data file ('.map' RUID converted)
Attached file
download raw data files ('.zip')
Attached file
download annotation files ('.zip')
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, 4μg 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 2µg 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 0.8µg 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 4µg 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 2µg 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 1.2µg of macaque total RNA extracted from ConA activated CD4+ T cells. MAC_unstim_1 was hybridized with RNA amplified from 1.2µg of macaque total RNA extracted from unstimulated CD4+ T cells. HUM_unstim_1 was hybridized with RNA amplified from 0.8µg of human total RNA extracted from unstimulated CD4+ T cells. The ABI microarrays AGM_tonsil and _brain were hybridized with RNA amplified from 0.8µg 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, Coppée JY, Barré-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