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]
expFile	TGCT.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_TGCT.mRNAseq_Preprocess.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00381:79	Methylation_Preprocess_2016012800	TGCT.meth.by_min_clin_corr.num_genes.txt	Methylation_Preprocessed	Level_3	txt	gdac.broadinstitute.org_TGCT.Methylation_Preprocess.Level_3.2016012800.0.0	yes
expFile	TGCT.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_TGCT.mRNAseq_Preprocess.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00381:79	Methylation_Preprocess_2016012800	TGCT.meth.by_min_clin_corr.data.txt	Methylation_Preprocessed	Level_3	txt	gdac.broadinstitute.org_TGCT.Methylation_Preprocess.Level_3.2016012800.0.0	yes
expFile	TGCT.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_TGCT.mRNAseq_Preprocess.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00381:79	Methylation_Preprocess_2016012800	TGCT.meth.by_max_stddev.data.txt	Methylation_Preprocessed	Level_3	txt	gdac.broadinstitute.org_TGCT.Methylation_Preprocess.Level_3.2016012800.0.0	yes
expFile	TGCT.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_TGCT.mRNAseq_Preprocess.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00381:79	Methylation_Preprocess_2016012800	TGCT.meth.by_mean.num_genes.txt	Methylation_Preprocessed	Level_3	txt	gdac.broadinstitute.org_TGCT.Methylation_Preprocess.Level_3.2016012800.0.0	yes
expFile	TGCT.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_TGCT.mRNAseq_Preprocess.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00381:79	Methylation_Preprocess_2016012800	TGCT.meth.by_mean.data.txt	Methylation_Preprocessed	Level_3	txt	gdac.broadinstitute.org_TGCT.Methylation_Preprocess.Level_3.2016012800.0.0	yes
expFile	TGCT.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_TGCT.mRNAseq_Preprocess.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00381:79	Methylation_Preprocess_2016012800	TGCT.meth.by_min_expr_corr.num_genes.txt	Methylation_Preprocessed	Level_3	txt	gdac.broadinstitute.org_TGCT.Methylation_Preprocess.Level_3.2016012800.0.0	yes
expFile	TGCT.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_TGCT.mRNAseq_Preprocess.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00381:79	Methylation_Preprocess_2016012800	TGCT.meth.by_min_expr_corr.data.txt	Methylation_Preprocessed	Level_3	txt	gdac.broadinstitute.org_TGCT.Methylation_Preprocess.Level_3.2016012800.0.0	yes
expFile	TGCT.uncv2.mRNAseq_RSEM_normalized_log2.txt	gdac.broadinstitute.org_TGCT.mRNAseq_Preprocess.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00381:79	Methylation_Preprocess_2016012800	TGCT.meth.by_max_stddev.num_genes.txt	Methylation_Preprocessed	Level_3	txt	gdac.broadinstitute.org_TGCT.Methylation_Preprocess.Level_3.2016012800.0.0	yes
inFile	TGCT.methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.data.txt	gdac.broadinstitute.org_TGCT.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00381:79	Methylation_Preprocess_2016012800	TGCT.meth.by_min_clin_corr.num_genes.txt	Methylation_Preprocessed	Level_3	txt	gdac.broadinstitute.org_TGCT.Methylation_Preprocess.Level_3.2016012800.0.0	yes
inFile	TGCT.methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.data.txt	gdac.broadinstitute.org_TGCT.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00381:79	Methylation_Preprocess_2016012800	TGCT.meth.by_min_clin_corr.data.txt	Methylation_Preprocessed	Level_3	txt	gdac.broadinstitute.org_TGCT.Methylation_Preprocess.Level_3.2016012800.0.0	yes
inFile	TGCT.methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.data.txt	gdac.broadinstitute.org_TGCT.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00381:79	Methylation_Preprocess_2016012800	TGCT.meth.by_max_stddev.data.txt	Methylation_Preprocessed	Level_3	txt	gdac.broadinstitute.org_TGCT.Methylation_Preprocess.Level_3.2016012800.0.0	yes
inFile	TGCT.methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.data.txt	gdac.broadinstitute.org_TGCT.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00381:79	Methylation_Preprocess_2016012800	TGCT.meth.by_mean.num_genes.txt	Methylation_Preprocessed	Level_3	txt	gdac.broadinstitute.org_TGCT.Methylation_Preprocess.Level_3.2016012800.0.0	yes
inFile	TGCT.methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.data.txt	gdac.broadinstitute.org_TGCT.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00381:79	Methylation_Preprocess_2016012800	TGCT.meth.by_mean.data.txt	Methylation_Preprocessed	Level_3	txt	gdac.broadinstitute.org_TGCT.Methylation_Preprocess.Level_3.2016012800.0.0	yes
inFile	TGCT.methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.data.txt	gdac.broadinstitute.org_TGCT.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00381:79	Methylation_Preprocess_2016012800	TGCT.meth.by_min_expr_corr.num_genes.txt	Methylation_Preprocessed	Level_3	txt	gdac.broadinstitute.org_TGCT.Methylation_Preprocess.Level_3.2016012800.0.0	yes
inFile	TGCT.methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.data.txt	gdac.broadinstitute.org_TGCT.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00381:79	Methylation_Preprocess_2016012800	TGCT.meth.by_min_expr_corr.data.txt	Methylation_Preprocessed	Level_3	txt	gdac.broadinstitute.org_TGCT.Methylation_Preprocess.Level_3.2016012800.0.0	yes
inFile	TGCT.methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.data.txt	gdac.broadinstitute.org_TGCT.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00381:79	Methylation_Preprocess_2016012800	TGCT.meth.by_max_stddev.num_genes.txt	Methylation_Preprocessed	Level_3	txt	gdac.broadinstitute.org_TGCT.Methylation_Preprocess.Level_3.2016012800.0.0	yes