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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 08, 2006 |
| Title |
MicroArray Quality Control (MAQC) Project |
| Organisms |
Homo sapiens; Rattus norvegicus |
| Experiment type |
Expression profiling by array
Expression profiling by RT-PCR
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| Summary |
Microarray technology has had a profound impact on gene expression research. Some studies have questioned whether similar expression results are obtained when the same RNA samples are analyzed on different platforms.
The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and analysis issues. We demonstrate the consistency of results within a platform across test sites as well as the high level of cross-platform concordance in terms of genes identified as differentially expressed. The MAQC study provides a rich resource that will help build consensus on the use of microarrays in research, clinical and regulatory settings. Manuscripts related to the MAQC project have been published in Nature Biotechnology, 24(9), September, 2006. More information about the MAQC project can be found at http://edkb.fda.gov/MAQC/.
Keywords: Cross-platform comparison
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| Overall design |
Expression data from two distinct reference RNA samples (A and B) in four titration pools were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Sample A = Stratagene Universal Human Reference RNA (UHRR, Catalog #740000), Sample B = Ambion Human Brain Reference RNA (HBRR, Catalog #6050), Sample C = Samples A and B mixed at 75%:25% ratio (A:B); and Sample D = Samples A and B mixed at 25%:75% ratio (A:B). In general, each microarray platform was tested at three sites and each sample was tested in five replicates at each test site. Samples (hybridizations) were named according to the following convention: Platform_Testsite_SampleRelicate. For example, AFX_2_B1 represents the hybridization (array) from platform AFX processed by test site 2 for the first replicate of sample B.
Assignment of platform code: ABI = Applied Biosystems (microarray); AFX = Affymetrix; AG1 = Agilent one-color; AGL = Agilent two-color; GEH = GE Healthcare; ILM = Illumina; NCI = NCI two-color (Operon oligos); EPP = Eppendorf; TAQ = TaqMan (Applied Biosystems); QGN = QuantiGene (Panomics); GEX = StaRT-PCR (Gene Express); H25K = TeleChem two-color; H25K1 = TeleChem one-color; BIO = CapitalBio two-color (Operon oligos); BIO1 = CapitalBio one-color (Operon oligos); OPN = Operon two-color (Operon oligos); NMC = Norwegian Microarray Consortium two-color (Operon oligos).
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| Contributor(s) |
Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Slikker W Jr |
| Citation(s) |
16964229, 20946593, 25150837, 25633159 |
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| Submission date |
Jul 19, 2006 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Leming Shi |
| E-mail(s) |
lemingshi@fudan.edu.cn
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| Phone |
+86-18616827008
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| Organization name |
Fudan University
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| Department |
School of Life Sciences
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| Lab |
Center for Pharmacogenomics
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| Street address |
2005 Songhu Road
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| City |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
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| Platforms (19)
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| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
| GPL1355 |
[Rat230_2] Affymetrix Rat Genome 230 2.0 Array |
| GPL1708 |
Agilent-012391 Whole Human Genome Oligo Microarray G4112A (Feature Number version) |
| GPL2507 |
Sentrix Human-6 Expression BeadChip |
| GPL2877 |
Agilent-013162 Whole Rat Genome Microarray G4131A (Feature Number version) |
| GPL2895 |
GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray |
| GPL2896 |
GE Healthcare/Amersham Biosciences CodeLink™ Rat Whole Genome Bioarray |
| GPL2986 |
ABI Human Genome Survey Microarray Version 2 |
| GPL2996 |
ABI Rat Genome Survey Microarray |
| GPL4096 |
Eppendorf DualChip Human MAQC (EPP) |
| GPL4097 |
TaqMan Human MAQC (TAQ) |
| GPL4098 |
Panomics Human MAQC (QGN) |
| GPL4108 |
NCI Operon Human MAQC |
| GPL4185 |
NCI Operon (second printing) Human MAQC |
| GPL4186 |
NMC (Norwegian Microarray Consortium) Operon Human MAQC |
| GPL4187 |
CapitalBio Operon Human MAQC (BIO and BIO1, two- and one-color) |
| GPL4188 |
Operon Human MAQC (OPN) |
| GPL4198 |
Gene Express StaRT-PCR (GEX) Human MAQC |
| GPL4219 |
TeleChem ArrayIt Human Microarrays for MAQC (H25K and H25K1 , two- and one-color) |
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| Samples (943)
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| Relations |
| BioProject |
PRJNA96213 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE5350_MAQC_ABI_123_60TXTs.zip |
17.1 Mb |
(ftp)(http) |
ZIP |
| GSE5350_MAQC_AFX_123456_120CELs.zip |
670.3 Mb |
(ftp)(http) |
ZIP |
| GSE5350_MAQC_AG1_123_60TXTs.zip |
413.6 Mb |
(ftp)(http) |
ZIP |
| GSE5350_MAQC_AGL_123_60TXTs.zip |
745.7 Mb |
(ftp)(http) |
ZIP |
| GSE5350_MAQC_BIO1_1_10LSRs.zip |
8.1 Mb |
(ftp)(http) |
ZIP |
| GSE5350_MAQC_BIO_1_20LSRs.zip |
33.4 Mb |
(ftp)(http) |
ZIP |
| GSE5350_MAQC_EPP_123_180TXTGPRs.zip |
24.7 Mb |
(ftp)(http) |
ZIP |
| GSE5350_MAQC_GEH_1232Fail_80TXTs.zip |
552.4 Mb |
(ftp)(http) |
ZIP |
| GSE5350_MAQC_H25K1_123_30GPRs.zip |
48.3 Mb |
(ftp)(http) |
ZIP |
| GSE5350_MAQC_H25K_2_30GPRs.zip |
88.9 Mb |
(ftp)(http) |
ZIP |
| GSE5350_MAQC_ILM_123_59TXTs.zip |
29.0 Mb |
(ftp)(http) |
ZIP |
| GSE5350_MAQC_NCI2nd_3r4_20GPRs.zip |
78.5 Mb |
(ftp)(http) |
ZIP |
| GSE5350_MAQC_NCI_122Fail3Fail_74GPRs.zip |
322.5 Mb |
(ftp)(http) |
ZIP |
| GSE5350_MAQC_NMC_1_10GPRs.zip |
38.5 Mb |
(ftp)(http) |
ZIP |
| GSE5350_MAQC_OPN_1_10GPRs.zip |
25.7 Mb |
(ftp)(http) |
ZIP |
| GSE5350_MAQC_Rat_180Files.zip |
680.1 Mb |
(ftp)(http) |
ZIP |
| GSE5350_MAQC_Tumor_20CELs.zip |
125.5 Mb |
(ftp)(http) |
ZIP |
| GSE5350_RAW.tar |
4.2 Gb |
(http)(custom) |
TAR (of CEL, CSV, GPR, LSR, TXT) |
| GSE5350_Summary_MAQC_DataSets.pdf |
39.8 Kb |
(ftp)(http) |
PDF |
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