Pipeline Input Name	Archive Result File REF	Comment [TCGA Archive Name]	Protocol REF	Data Transformation Name	Derived Data File	Comment [TCGA Data Type]	Comment [TCGA Data Level]	Comment [TCGA File Type]	Comment [TCGA Archive Name]	Comment [TCGA Include for Analysis]
GDAC_sampleFeature:cndel	del_genes.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.transferedsamplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:cndel	del_genes.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.samplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:cndel	del_genes.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:cndel	del_genes.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:cnamp	amp_genes.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.transferedsamplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:cnamp	amp_genes.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.samplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:cnamp	amp_genes.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:cnamp	amp_genes.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:clusters	MESO-TP.mergedcluster.txt	gdac.broadinstitute.org_MESO-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.transferedsamplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:clusters	MESO-TP.mergedcluster.txt	gdac.broadinstitute.org_MESO-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.samplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:clusters	MESO-TP.mergedcluster.txt	gdac.broadinstitute.org_MESO-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:clusters	MESO-TP.mergedcluster.txt	gdac.broadinstitute.org_MESO-TP.Aggregate_Molecular_Subtype_Clusters.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:mRNA	MESO-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_MESO-TP.mRNAseq_Preprocess.Level_3.2016012800.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.transferedsamplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:mRNA	MESO-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_MESO-TP.mRNAseq_Preprocess.Level_3.2016012800.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.samplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:mRNA	MESO-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_MESO-TP.mRNAseq_Preprocess.Level_3.2016012800.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:mRNA	MESO-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_MESO-TP.mRNAseq_Preprocess.Level_3.2016012800.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:cnbroad	broad_values_by_arm.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.transferedsamplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:cnbroad	broad_values_by_arm.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.samplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:cnbroad	broad_values_by_arm.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:cnbroad	broad_values_by_arm.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:cnfocal	all_lesions.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.transferedsamplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:cnfocal	all_lesions.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.samplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:cnfocal	all_lesions.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:cnfocal	all_lesions.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:genelist	cancergene_scna_all_2014_10_16.tsv	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.transferedsamplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:genelist	cancergene_scna_all_2014_10_16.tsv	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.samplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:genelist	cancergene_scna_all_2014_10_16.tsv	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:genelist	cancergene_scna_all_2014_10_16.tsv	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:broadq	broad_significance_results.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.transferedsamplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:broadq	broad_significance_results.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.samplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:broadq	broad_significance_results.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:broadq	broad_significance_results.txt	gdac.broadinstitute.org_MESO-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:mRNAmarkergene	MESO-TP.subclassmarkers.txt	gdac.broadinstitute.org_MESO-TP.mRNAseq_Clustering_CNMF.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.transferedsamplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:mRNAmarkergene	MESO-TP.subclassmarkers.txt	gdac.broadinstitute.org_MESO-TP.mRNAseq_Clustering_CNMF.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.samplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:mRNAmarkergene	MESO-TP.subclassmarkers.txt	gdac.broadinstitute.org_MESO-TP.mRNAseq_Clustering_CNMF.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:mRNAmarkergene	MESO-TP.subclassmarkers.txt	gdac.broadinstitute.org_MESO-TP.mRNAseq_Clustering_CNMF.Level_4.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:clinical	MESO-TP.merged_data.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.transferedsamplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:clinical	MESO-TP.merged_data.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	MESO-TP.samplefeatures.txt	sampleFeatureTable	Level_4	txt	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:clinical	MESO-TP.merged_data.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
GDAC_sampleFeature:clinical	MESO-TP.merged_data.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10897:44	Aggregate_AnalysisFeatures_2016012800	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_MESO-TP.Aggregate_AnalysisFeatures.Level_4.2016012800.0.0	yes
