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A copy of the data is available from the TranSMART Foundation library server

See also the Tutorial: How to load the Cell Line Use Case dataset with transmart-data.

Data TypeSubset SubjectsPlatformDescriptionSourceLoad target
clinical Single set19 -Clinical dataCTMM TraIT 
aCGHregions 180k5180k region Copy number variation dataCTMM TraIT 
aCGHregions 224k10224k regionaCGH dataCTMM TraIT 
aCGH genes 180k5GPL8687aCGH dataCTMM TraIT 
aCGHgenes 224k10GPL8687aCGH dataCTMM TraIT 
expressionAffymetrix exon array2Affymetrix exon arrayexpression dataCTMM TraIT 
expressionAgilent 4k mRNA microarray16Agilent 4k mRNA microarrayexpression dataCTMM TraIT 
mirna_qpcrMicroRNA qPCR data2Cell-line mirnamiRNA qPCR dataCTMM TraIT 
proteomicsProteomics data8Cell-line proteomicsMass-spec proteomics dataCTMM TraIT 
rnaseqIllumina GA II6IlluminaRNAseq dataCTMM TraIT 
rnaseqIllumina HiSeq2000 Untreated 11IlluminaRNAseq dataCTMM TraIT 
rnaseqIllumina HiSeq2000 Untreated 21IlluminaRNAseq dataCTMM TraIT 
rnaseqIllumina HiSeq2000 DMSO control 11IlluminaRNAseq dataCTMM TraIT 
rnaseqIllumina HiSeq2000 DMSO control 21IlluminaRNAseq dataCTMM TraIT 
rnaseqIllumina HiSeq2000 siNon-Targeting 11IlluminaRNAseq dataCTMM TraIT 
rnaseqIllumina HiSeq2000 siNon-Targeting 21IlluminaRNAseq dataCTMM TraIT 
vcfComplete genomics DNAseq 2-Genomic variation dataCTMM TraIT 
vcfIllumina GA II RNAseq6-Variation data from RNAseqCTMM TraIT 
vcfIllumina HiSeq2000 RNAseq Untreated 11-Variation data from RNAseqCTMM TraIT 
vcfIllumina HiSeq2000 RNAseq Untreated 21-Variation data from RNAseqCTMM TraIT 
vcfIllumina HiSeq2000 RNAseq DMSO control 11-Variation data from RNAseqCTMM TraIT 
vcfIllumina HiSeq2000 RNAseq  DMSO control 21-Variation data from RNAseqCTMM TraIT 
vcfIllumina HiSeq2000 RNAseq siNon-Targeting 11-Variation data from RNAseqCTMM TraIT 
vcfIllumina HiSeq2000 RNAseq siNon-Targeting 21-Variation data from RNAseqCTMM TraIT 

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Some datasets (e.g. KEGG) can only be used with an appropriate license.

The scripts on the test servers use the loader in tranSMART-ETL which has been tested on both Postgres and Oracle.

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CTMM TraIT has brought together a diverse set of data from 6 different cell lines under the Cell Line use case, to test tranSMART on public data without complicated privacy regulations.  A detailed tutorial can be found here: Tutorial: How to load the Loading data with transmart-data (Cell Line Use Case dataset with transmart-data).

eTRIKS

The eTRIKS project has over 50 curated studies loaded in the public eTRIKS server: https://public.etriks.org/. This includes both clinical and mRNA gene expression data fro GEO studies plus studies from The Cancer Genome Atlas (TCGA) and other sources.

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