Platform Design

Center TCGA Platform Code DCC Platform Name Instrument Support Materials Sequence Download TCGA ADF Download
Broad Institute of MIT and Harvard ABI Applied Biosystems Sequence data Applied Biosystems DNA Analyzers Primers N/A
McDonnell Genome Institute at Washington University ABI Applied Biosystems Sequence data Applied Biosystems DNA Analyzers Primers N/A
Human Genome Sequencing Center at Baylor College of Medicine ABI Applied Biosystems Sequence data Applied Biosystems DNA Analyzers Primers N/A
University of North Carolina AgilentG4502A_07_1 Agilent 244K Custom Gene Expression G4502A-07-1 Agilent SurePrint G3 Microarray Platform FASTA TCGA ADF
University of North Carolina AgilentG4502A_07_2 Agilent 244K Custom Gene Expression G4502A-07-2 Agilent SurePrint G3 Microarray Platform FASTA TCGA ADF
University of North Carolina AgilentG4502A_07_3 Agilent 244K Custom Gene Expression G4502A-07-3 Agilent SurePrint G3 Microarray Platform FASTA TCGA ADF
Memorial Sloan Kettering Cancer Center CGH-1x1M_G4447A Agilent SurePrint G3 Human CGH Microarray Kit 1x1M Agilent SurePrint G3 Microarray Platform FASTA TCGA ADF
Broad Institute of MIT and Harvard Genome_Wide_SNP_6 Affymetrix Genome-Wide Human SNP Array 6.0 Affymetrix Genome-Wide Human SNP Array 6.0 FASTA TCGA ADF
McDonnell Genome Institute at Washington University Genome_Wide_SNP_6 Affymetrix Genome-Wide Human SNP Array 6.0 Affymetrix Genome-Wide Human SNP Array 6.0 FASTA TCGA ADF
University of North Carolina H-miRNA_8x15K Agilent 8 x 15K Human miRNA-specific microarray Agilent miRNA Microarray FASTA TCGA ADF
University of North Carolina H-miRNA_8x15Kv2 Agilent Human miRNA Microarray Rel12.0 Agilent miRNA Microarray FASTA TCGA ADF
Memorial Sloan Kettering Cancer Center HG-CGH-244A Agilent Human Genome CGH Microarray 244A Agilent SurePrint G3 Microarray Platform FASTA TCGA ADF
Harvard Medical School HG-CGH-244A Agilent Human Genome CGH Microarray 244A Agilent SurePrint G3 Microarray Platform FASTA TCGA ADF
Harvard Medical School HG-CGH-415K_G4124A Agilent Human Genome CGH Custom Microarray 2x415K Agilent SurePrint G3 Microarray Platform FASTA TCGA ADF
McDonnell Genome Institute at Washington University HG-U133_Plus_2 Affymetrix Human Genome U133 Plus 2.0 Array Affymetrix Human Genome U133 Array FASTA TCGA ADF
Broad Institute of MIT and Harvard HT_HG-U133A Affymetrix HT Human Genome U133 Array Plate Set Affymetrix Human Genome U133 Array FASTA TCGA ADF
Berkeley Lab HuEx-1_0-st-v2 Affymetrix Human Exon 1.0 ST Array Affymetrix Exon Array FASTA TCGA ADF
HudsonAlpha Institute for Biotechnology Human1MDuo Illumina Human1M-Duo BeadChip Illumina DNA BeadChip FASTA TCGA ADF
HudsonAlpha Institute for Biotechnology HumanHap550 Illumina 550K Infinium HumanHap550 SNP Chip Illumina Infinium HumanHap550 SNP Chip FASTA TCGA ADF
Johns Hopkins - USC Epigenome Center HumanMethylation27 Illumina Infinium Human DNA Methylation 27 Illumina Infinium Human DNA Methylation 27 See ADF File TCGA ADF
Johns Hopkins - USC Epigenome Center HumanMethylation450 Illumina Infinium Human DNA Methylation 450 Illumina Infinium Human DNA Methylation 450 See ADF File TCGA ADF
Johns Hopkins - USC Epigenome Center IlluminaDNAMethylation_OMA002_CPI Illumina DNA Methylation OMA002 Cancer Panel I Illumina DNA Methylation Cancer Panel FASTA TCGA ADF
Johns Hopkins - USC Epigenome Center IlluminaDNAMethylation_OMA003_CPI Illumina DNA Methylation OMA003 Cancer Panel I Illumina DNA Methylation Cancer Panel See ADF File TCGA ADF
McDonnell Genome Institute at Washington University IlluminaGA_DNASeq Illumina Genome Analyzer DNA Sequencing Illumina Genome Analyzer IIx N/A N/A
Broad Institute of MIT and Harvard IlluminaGA_DNASeq Illumina Genome Analyzer DNA Sequencing Illumina Genome Analyzer IIx N/A N/A
Human Genome Sequencing Center at Baylor College of Medicine IlluminaGA_DNASeq Illumina Genome Analyzer DNA Sequencing Illumina Genome Analyzer IIx N/A N/A
University of California Santa Cruz IlluminaGA_DNASeq Illumina Genome Analyzer DNA Sequencing Illumina Genome Analyzer IIx N/A N/A
University of North Carolina IlluminaGA_DNASeq Illumina Genome Analyzer DNA Sequencing Illumina Genome Analyzer IIx N/A N/A
BC Cancer Agency IlluminaGA_miRNASeq Illumina Genome Analyzer miRNA Sequencing Illumina Genome Analyzer IIx N/A N/A
Harvard Medical School IlluminaGA_mRNA_DGE Illumina Genome Analyzer mRNA Digital Gene Expression Illumina Genome Analyzer IIx N/A N/A
BC Cancer Agency IlluminaGA_RNASeq Illumina Genome Analyzer RNA Sequencing Illumina Genome Analyzer IIx N/A N/A
University of North Carolina IlluminaGA_RNASeqV2 Illumina Genome Analyzer RNA Sequencing Version 2 analysis Illumina Genome Analyzer IIx N/A N/A
Harvard Medical School IlluminaHiSeq_DNASeqC Illumina HiSeq for Copy Number Variation Illumina HiSeq 2000 N/A N/A
BC Cancer Agency IlluminaHiSeq_miRNASeq Illumina HiSeq 2000 miRNA Sequencing Illumina HiSeq 2000 N/A N/A
University of North Carolina IlluminaHiSeq_RNASeq Illumina HiSeq 2000 RNA Sequencing Illumina HiSeq 2000 N/A N/A
University of North Carolina IlluminaHiSeq_RNASeqV2 Illumina HiSeq 2000 RNA Sequencing Version 2 analysis Illumina HiSeq 2000 N/A N/A
University of North Carolina IlluminaHiSeq_TotalRNASeqV2 Illumina HiSeq 2000 Total RNA Sequencing Version 2 analysis Illumina HiSeq 2000 N/A N/A
Johns Hopkins - USC Epigenome Center IlluminaHiSeq_WGBS Illumina HiSeq 2000 Bisulfite-converted DNA Sequencing Illumina HiSeq 2000 N/A N/A
MD Anderson Cancer Center MDA_RPPA_Core M.D. Anderson Reverse Phase Protein Array Core M.D. Anderson Reverse Phase Protein Array Core N/A N/A
Nationwide Children's Hospital microsat_i Microsatellite Instability Analysis ABI SOLiD System Sequencing N/A N/A
University of California Santa Cruz SOLiD_DNASeq ABI SOLiD DNA System Sequencing ABI SOLiD System Sequencing N/A N/A
Broad Institute of MIT and Harvard SOLiD_DNASeq ABI SOLiD DNA System Sequencing ABI SOLiD System Sequencing N/A N/A
Human Genome Sequencing Center at Baylor College of Medicine SOLiD_DNASeq ABI SOLiD DNA System Sequencing ABI SOLiD System Sequencing N/A N/A

Center: Provides the name of the center that submitted data for a particular platform. A report is available that provides a relationship between the center name, center type, center display name, and BCR center ID (data generating center).

TCGA Platform Code: Provides the code used in The Cancer Genome Atlas (TCGA) to represent a platform. The platform code is used in archive and file names as well as file contents. A report is available that provides the relationship between the TCGA Platform Code and Platform Name.

Instrument Support Materials: Provides the vendor's name of a particular platform. The platform name links to the best information available about how that platform works and its support materials. If these materials do not address a specific question related to the platform, we recommend you contact the vendor directly.

Sequence Download: The links provided in this column either download the FASTA file that was submitted by the related center and used to create the ADF file, or in the case of sequence-based platforms, take you to the National Center for Biotechnology Information (NCBI) Trace or Short Read Archives where you can download or search the metadata to get the primers used in the assay. Values of "N/A" mean that probe or primer sequence files are not applicable to the related platform and that those sequences may be available in a result file (e.g. IlluminaGA_mRNA_DGE sequences are available in the archive result files).

TCGA ADF Download: TCGA uses a modified format of the standard MAGE ADF file. TCGA ADFs are used in the analysis of the resulting data. The links provided download the TCGA ADF. Values of "N/A" mean that ADF files are not applicable to the related platform (e.g. IlluminaGA_mRNA_DGE is not an array-based platform and so has no ADF).