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]
ga2file	STAD.rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.data.txt	gdac.broadinstitute.org_STAD.Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.Level_3.2013101000.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10090:32	mRNAseq_Preprocess_2013101000	STAD.mRNAseq_RPKM.txt	Expression_mRNAseq	Level_4	txt	gdac.broadinstitute.org_STAD.mRNAseq_Preprocess.Level_4.2013101000.0.0	yes
ga2file	STAD.rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.data.txt	gdac.broadinstitute.org_STAD.Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.Level_3.2013101000.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10090:32	mRNAseq_Preprocess_2013101000	stderr.txt	Expression_mRNAseq	Level_4	txt	gdac.broadinstitute.org_STAD.mRNAseq_Preprocess.Level_4.2013101000.0.0	yes
ga2file	STAD.rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.data.txt	gdac.broadinstitute.org_STAD.Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.Level_3.2013101000.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10090:32	mRNAseq_Preprocess_2013101000	STAD.mRNAseq_RPKM_log2.txt	Expression_mRNAseq	Level_4	txt	gdac.broadinstitute.org_STAD.mRNAseq_Preprocess.Level_4.2013101000.0.0	yes
ga2file	STAD.rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.data.txt	gdac.broadinstitute.org_STAD.Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.Level_3.2013101000.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10090:32	mRNAseq_Preprocess_2013101000	stdout.txt	Expression_mRNAseq	Level_4	txt	gdac.broadinstitute.org_STAD.mRNAseq_Preprocess.Level_4.2013101000.0.0	yes
ga2file	STAD.rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.data.txt	gdac.broadinstitute.org_STAD.Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.Level_3.2013101000.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10090:32	mRNAseq_Preprocess_2013101000	STAD.mRNAseq_raw_counts.txt	Expression_mRNAseq	Level_4	txt	gdac.broadinstitute.org_STAD.mRNAseq_Preprocess.Level_4.2013101000.0.0	yes
ga2file	STAD.rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.data.txt	gdac.broadinstitute.org_STAD.Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.Level_3.2013101000.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10090:32	mRNAseq_Preprocess_2013101000	STAD.mRNAseq_RPKM_log2_PARADIGM.txt	Expression_mRNAseq	Level_4	txt	gdac.broadinstitute.org_STAD.mRNAseq_Preprocess.Level_4.2013101000.0.0	yes
ga2file	STAD.rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.data.txt	gdac.broadinstitute.org_STAD.Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.Level_3.2013101000.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10090:32	mRNAseq_Preprocess_2013101000	STAD.mRNAseq_median_length_normalized.txt	Expression_mRNAseq	Level_4	txt	gdac.broadinstitute.org_STAD.mRNAseq_Preprocess.Level_4.2013101000.0.0	yes
hiseq	STAD.rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data.data.txt	gdac.broadinstitute.org_STAD.Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data.Level_3.2013101000.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10090:32	mRNAseq_Preprocess_2013101000	STAD.mRNAseq_RPKM.txt	Expression_mRNAseq	Level_4	txt	gdac.broadinstitute.org_STAD.mRNAseq_Preprocess.Level_4.2013101000.0.0	yes
hiseq	STAD.rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data.data.txt	gdac.broadinstitute.org_STAD.Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data.Level_3.2013101000.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10090:32	mRNAseq_Preprocess_2013101000	stderr.txt	Expression_mRNAseq	Level_4	txt	gdac.broadinstitute.org_STAD.mRNAseq_Preprocess.Level_4.2013101000.0.0	yes
hiseq	STAD.rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data.data.txt	gdac.broadinstitute.org_STAD.Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data.Level_3.2013101000.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10090:32	mRNAseq_Preprocess_2013101000	STAD.mRNAseq_RPKM_log2.txt	Expression_mRNAseq	Level_4	txt	gdac.broadinstitute.org_STAD.mRNAseq_Preprocess.Level_4.2013101000.0.0	yes
hiseq	STAD.rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data.data.txt	gdac.broadinstitute.org_STAD.Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data.Level_3.2013101000.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10090:32	mRNAseq_Preprocess_2013101000	stdout.txt	Expression_mRNAseq	Level_4	txt	gdac.broadinstitute.org_STAD.mRNAseq_Preprocess.Level_4.2013101000.0.0	yes
hiseq	STAD.rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data.data.txt	gdac.broadinstitute.org_STAD.Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data.Level_3.2013101000.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10090:32	mRNAseq_Preprocess_2013101000	STAD.mRNAseq_raw_counts.txt	Expression_mRNAseq	Level_4	txt	gdac.broadinstitute.org_STAD.mRNAseq_Preprocess.Level_4.2013101000.0.0	yes
hiseq	STAD.rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data.data.txt	gdac.broadinstitute.org_STAD.Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data.Level_3.2013101000.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10090:32	mRNAseq_Preprocess_2013101000	STAD.mRNAseq_RPKM_log2_PARADIGM.txt	Expression_mRNAseq	Level_4	txt	gdac.broadinstitute.org_STAD.mRNAseq_Preprocess.Level_4.2013101000.0.0	yes
hiseq	STAD.rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data.data.txt	gdac.broadinstitute.org_STAD.Merge_rnaseq__illuminahiseq_rnaseq__bcgsc_ca__Level_3__gene_expression__data.Level_3.2013101000.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:10090:32	mRNAseq_Preprocess_2013101000	STAD.mRNAseq_median_length_normalized.txt	Expression_mRNAseq	Level_4	txt	gdac.broadinstitute.org_STAD.mRNAseq_Preprocess.Level_4.2013101000.0.0	yes
