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Series GSE6982

Query DataSets for GSE6982

Status

Public on Oct 01, 2007

Title

Long Oligonucleotide Microarrays for African Green Monkey Gene Expression Profile Analysis

Platform organism

Homo sapiens

Sample organisms

Macaca mulatta; Homo sapiens; Chlorocebus sabaeus

Experiment type

Expression profiling by array

Summary

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

Overall design

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.

Contributor(s)

Jacquelin B, Mayau V, Brysbaert G, Regnault B, Diop OM, Arenzana-Seisdedos F, Rogge L, Coppee J, Barré-Sinoussi F, Benecke A, Müller-Trutwin MC

Citation(s)

17507667

Submission date

Feb 07, 2007

Last update date

Mar 25, 2019

Contact name

Beatrice JACQUELIN

E-mail(s)

beajac@pasteur.fr

Organization name

Institut Pasteur

Department

Virologie

Lab

Regulations des Infections Retrovirales

Street address

25 rue du Docteur Roux

City

Paris cedex 15

ZIP/Postal code

75724

Country

France

Platforms (3)

GPL570	[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
GPL1426	ABI Human Genome Survey Microarray Version 1
GPL2986	ABI Human Genome Survey Microarray Version 2

Samples (14)

More...

GSM160607	Circulating CD4+ T cells stimulated with ConA AGM_stim_1_AB
GSM160609	Circulating CD4+ T cells stimulated with ConA AGM_stim_2_AB
GSM160613	Circulating CD4+ T cells stimulated with ConA MAC_stim_1

Relations

BioProject

PRJNA99293

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE6982_RAW.tar	41.9 Mb	(http)(custom)	TAR (of CEL, EXP, TXT)