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Series GSE5350 Query DataSets for GSE5350
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
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
 
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).
 
Contributor(s) Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Slikker W Jr
Citation(s) 16964229, 20946593, 25150837, 25633159
Submission date Jul 19, 2006
Last update date Mar 25, 2019
Contact name Leming Shi
E-mail(s) leming.shi@gmail.com
Phone +86-18616827008
Organization name Fudan Univresity
Department School of Life Sciences
Lab Center for Pharmacogenomics
Street address 2005 Songhu Road
City Shanghai
ZIP/Postal code 200438
Country China
 
Platforms (19)
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)
Samples (943)
GSM122774 MAQC_AFX_1_A1
GSM122775 MAQC_AFX_1_A2
GSM122776 MAQC_AFX_1_A3
Relations
BioProject PRJNA96213

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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
Raw data provided as supplementary file

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