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Data Set Metadata

Provides background information about each data set. Check back for additional data sets as we make them available. Drug DNA RNA Protein

Drug

Name	Platform Information	Principal Collaborators	Data Description
NCI Almanac Data: Combo Scores [PMID:28446463]	Manufacturer: Developmental Therapeutics Program, NCI/NIH Platform: Sulforhodamine assay Molecular Target: Drug Platform Description: The selected drug pair represents the efficacy of the drug combination when tested against NCI's standard set of 60 cancer cell lines. Generally, a higher score value indicates the drug combination slowed the growth of a particular type of cancer more effectively than what would be expected, based on the performance of the drugs when tested separately. [data repository]	Developmental Therapeutics Program, DCTD, NCI, NIH (J Morris); Genomics and Pharmacology Facility DTB, CCR, NCI, NIH	Raw Data: Combo scores Processing method: sulforhodamine B total protein cytotoxicity assay, 48hrs post-treatment
Compound activity: DTP NCI-60 [PMID:22802077]	Manufacturer: Developmental Therapeutics Program, NCI/NIH Platform: Sulforhodamine assay Molecular Target: Drug Platform Description: Negative log10 (GI50) values of sulforhodamine B assay for ~ 50K compounds, including more than 20,000 that passed quality control, 158 Food and Drug Administration approved and 79 clinical trial drugs. Higher values equate to higher sensitivity of cell lines. [data repository] [Platform description]	LMP, CCR, NCI (K Kohn); DPT, NCI (J Morris); Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH	Raw Data: Compound activity data. All available replicates for each NSC are shown without the quality control steps performed for normalized data. Processing method: The quality control steps included in the NCI-60 Analysis Tools outputs for data reproducibility and minimum variability across cell lines are not included.

DNA

Name	Platform Information	Principal Collaborators	Data Description
DNA: Affy 500K SNP [PMID:24670534]	Manufacturer: Affymetrix, Inc Platform: GeneChip Human Mapping 500k Array Set Molecular Target: DNA Platform Description: This platform is used for whole-genome association studies. It is comprised of two arrays which enable genotyping of more than 500,000 single nucleotide polymorphisms (SNPs). [data repository] [Platform description]	Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH (W Reinhold); Gene Logic (E Kaljian)	Raw Data: Cel files Processing method: For SNP data, the CRLMM algorithm was used to do allelic cross talk calibration, base position normalization and RMA. For Array CGH, normalization was done using the CRMAv2 normalization. Both analyses were done using the aroma.affymetrix package in R.
DNA: Fingerprinting [PMID:19372543]	Manufacturer: Qiagen; Applied Biosystems Platform: AmpFLSTR Identifiler PCR Amplification kit Molecular Target: DNA Platform Description: DNA was prepared from cells using the Qiagen Blood & Cell Culture DNA Maxi kit according to the manufacturer's protocol (Qiagen, Valencia, CA). DNA fingerprints were obtained for all cell lines using the AmpFLSTR Identifiler PCR Amplification kit (Applied Biosystems, Foster City, CA) according to the manufacturer's protocol [data repository] [Platform description]	Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH (P Lorenzi, S Varma, W Reinhold)	Raw Data: Number of Short Tandem Repeats (STR) at 13 combined DNA index system (CODIS) loci, the amelogenin gender-determining marker used in forensics, and two Processing method: NA
DNA: E-cadherin Methylation [PMID:17272646]	Manufacturer: NA Platform: PCR amplification and sequencing of sodium bisulfite modified DNA. Molecular Target: DNA methylation status of E-cadherin promoter. Platform Description: Genomic DNA (5 micrograms) from each cell line was treated with sodium bisulfite at 50 degrees C for 17 hr. The DNA was then re-suspended in 125 microliters of 10-mM Tris with 1 mM EDTA pH 7.4. Nested PCR amplification and sequencing of the DNA were carried out using either converted or unconverted DNA as template for the PCR. Primers were based on the E-cad promoter DNA sequence (GenBank accession no. L34545). One-strand automated sequencing of the PCR products was performed. For primers and more detailed information see citation. [data repository] [Platform description]	Gene Logic (D Dolginow), SAIC (D Munroe), Johns Hopkins Univ. (A Feinberg); Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH (W Reinhold)	Raw Data: sequence tracings Processing method: Multiple sequence tracings were grouped by bisulfite conversion and sequencing date, calculated as a group mean for each CpG within these groups, and then combined as a mean of these groups.
DNA: Exome Seq [PMID:23856246]	Manufacturer: Illumina Platform: Genome Analyzer Molecular Target: DNA Platform Description: High throughput sequencing of NCI-60 for SNPs/variants [data repository] [Platform description]	Genetics Branch, CCR, NCI, NIH (O Abaan, S Davis, P Meltzer); Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH (W Reinhold, Y Pommier); Division of Cancer Treatment and Diagnosis, NCI, NIH (S Holbeck, R Simon, J Doroshow)	Raw Data: FASTQ Sequence File Processing method: Segmental duplications and those variants that map to more than one genomic location have been removed.
DNA: Illumina 1M SNP [PMID:24670534]	Manufacturer: Illumina Platform: Human 1M-Duo Beadchip Molecular Target: DNA Platform Description: BeadChip array based on Illumina's Infinium Assay with probes for 1072820 SNPs [data repository] [Platform description]	Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH	Raw Data: Red and Green IDAT files for each cell line Processing method:
DNA: Roche NimbleGen 385k aCGH [PMID:20215517]	Manufacturer: Roche NimbleGen Systems, Inc Platform: HG19 CGH 385K WG Tiling v2.0 Molecular Target: DNA Platform Description: See link below. [data repository] [Platform description]	Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH	Raw Data: PAIR files Processing method: Subtracted estimate of probe bias for each probe. A detailed explanation of the probe bias calculation is included with the normalized download.
DNA: Sanger sequencing [PMID:17088437]	Manufacturer: ABI 3730 Sequencer Platform: Sequencing Molecular Target: DNA Platform Description: Sequencing of the NCI-60 for mutations in known human cancer genes. The coding exons and immediate flanking intron sequences of selected genes from the Cancer Gene Census were PCR-amplified and sequenced. [data repository] [Platform description]	Wellcome Trust Sanger Institute (M Stratton); Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH	Raw Data: NA Base-calling method: Mutation surveyor, Chromas, in-house Sanger software
DNA: Illumina 450K methylation	Manufacturer: Illumina Platform: Infinium HumanMethylation450 BeadChip Kit Molecular Target: DNA Platform Description: Approximately 450,000 probes querying the methylation status of CpG sites within and outside of genes. [data repository] [Platform description]	Manel Esteller (Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL)), Paul Meltzer (NCI)	Raw Data: Processing method: Beta values normalized to a value between 0 (unmethylated) and 1 (methylated) using the R methylumi package
DNA: Combined aCGH [PMID:24670534]	Manufacturer: See individual platform information Platform: Probe intensities combined from four platforms Molecular Target: DNA Platform Description: Probe intensities combined from four platforms: Agilent Human Genome CGH Microarray 44A, Nimblegen HG19 CGH 385K WG Tiling v2.0, Affymetrix GeneChip Human Mapping 500k Array Set and Illumina Human1Mv1_C Beadchip [data repository] [Platform description]	See individual platform information	Raw Data: See individual platform information Base-calling method: NA
DNA: aCGH Agilent 44K [PMID:24670534]	Manufacturer: Agilent Technologies, Inc. Platform: Human Genome CGH Microarray 44A and 44B Molecular Target: DNA Platform Description: A genome-wide DNA copy number variation profiling array containing 43,000 plus human sequences from both coding and non-coding regions. [data repository] [Platform description]	Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH (W Reinhold)	Raw Data: ratio of sample vs control of DNA copy number, normal female DNA 46,XX genomic DNA was obtained from Promega (Madison, WI) Processing method: Agilent Feature Extraction done with software version 8.1 with default settings for CGH arrays.

RNA

Name	Platform Information	Principal Collaborators	Data Description
RNA: Agilent Human microRNA (V2) [PMID:20442302]	Manufacturer: Agilent Technologies Platform: Human miRNA Microarray (V2) Molecular Target: RNA Platform Description: 15,000 probes for 723 human and 76 human viral miRNA's. Each slide contains 8 arrays. [data repository] [Platform description]	Agilent Technologies (S Fulmer-Smentek, P D'Andrade); Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH	Raw Data: Data in tab delimited text files. Array quality information as PDF files Processing method: GreenSpringGX MicroRNA location based on HG18
RNA: 5 Platform Gene Transcript [PMID:21159603]	Manufacturer: See individual platform information Platform: Expression values combined from five platforms Molecular Target: RNA Platform Description: Expressions from five platforms (Affymetrix: HG-U95; HG-U133; HG-U133 Plus 2.0; HG Exon 1.0 ST. Agilent: Whole Human Genome Oligo array) were combined. [data repository] [Platform description]	See individual platform information	Raw Data: See individual platform information Processing method: Expression values for each gene were converted to z-scores. Probes from the 5 platforms that correspond to the gene were selected based on a QC step. The average z-score using the selected probes was reported as the combined gene expression for the gene.
RNA: RNA-seq [PMID:31113817]	Manufacturer: Illumina Platform: HiSeq 2000 Molecular Target: RNA Platform Description: High throughput sequencing of NCI-60 transcripts. [data repository] [Platform description]	Genetics Branch, NCI, NIH (O Abaan, S Davis, P Meltzer); Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH (W Reinhold, Y Pommier); Division of Cancer Treatment and Diagnosis, NCI, NIH (S Holbeck, R Simon, J Doroshow)	Raw Data: sequence tracings Processing method: RNA was quantified and treated with DNAse according to the manufacturers protocol (Qiagen, Inc). RNA was used for generating sequencing libraries using the TotalScript™ RNA-Seq Kit (Epicentre). The libraries were sequenced at the Center for Cancer Research Sequencing facility using the HiSeq 2000 (Illumina) using the TruSeq Cluster Kit v3 (Illumina). Data was converted to fastq and aligned back to the human genome assembly 19 with the STAR split-read aligner. RNAseQC was used to analyze the data files to determine the data quality.
RNA: OSU Transporter Array [PMID:15205344]	Manufacturer: Ohio State University Platform: Spotted Array Molecular Target: RNA Platform Description: Spotted 70-mer microarray [data repository] [Platform description]	OSU (W Sadee); Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH	Raw Data: Processing method: Normalization based on robust, locally linear fits (Loess), implemented in the SMA R package
RNA: microRNA OSU V3 chip [PMID:17483436]	Manufacturer: Ohio State University Comprehensive Cancer Center Platform: OSU-CCC_hsa-miRNA-chip_v3 For array design, see: V3 design protocol A-MEXP-620 published on ArrayExpress (www.ebi.ac.uk/arrayexpress/) Molecular Target: RNA Platform Description: See: Liu CG, Calin GA, Meloon B, Gamliel N, Sevignani C, Ferracin M, Dumitru CD, Shimizu M, Zupo S, Dono M, Alder H, Bullrich F, Negrini M, and Croce CM. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci U S A 2004;101:9740-4. [data repository] [Platform description]	CCC, OSU (P Blower); Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH	Raw Data: Two channel sample and background intensity measurements. Processing method: Human probes were selected and expression was measured as the log of the median signal intensity minus background (thresholded to a minimum of 1) and duplicate spots were averaged. Each sample was quantile normalized and the replicates averaged for each cell line.
RNA: Agilent mRNA [PMID:20442302]	Manufacturer: Agilent Technologies Platform: Whole Human Genome Microarray, 4 x 44K Molecular Target: RNA Platform Description: 44,000 Probes for approximately 41,000 genes, with 4 arrays spotted on each slide. [data repository] [Platform description]	Agilent Technologies (S Fulmer-Smentek, P D'Andrade); Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH (W Reinhold)	Raw Data: Text files with data and PDF files with quality information Processing method: Processed using GeneSpring
RNA: Affy HuEx 1.0 [PMID:20215517]	Manufacturer: Affymetrix, Inc Platform: GeneChip Human Exon 1.0 ST Molecular Target: RNA Platform Description: 1432155 probesets for all human gene exons [data repository] [Platform description]	Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH (W Reinhold); Affymetrix (T Gingeras); GeneLogic (E Kaldjian); MD Anderson (J Weinstein)	Raw Data: cel files Processing method: GCRMA
RNA: Affy HG-U133 Plus 2.0 [PMID:20215517]	Manufacturer: Affymetrix, Inc Platform: Human Genome U133 Plus 2.0 Molecular Target: RNA Platform Description: Aproximately 47,000 transcripts. For more detail see link below. [data repository] [Platform description]	Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH (W Reinhold)	Raw Data: cel files Processing method: GCRMA, RMA 59 cell lines - ME:MDA_N is excluded
RNA: Affy HG-U133(A-B) [PMID:17339364]	Manufacturer: Affymetrix, Inc Platform: Human Genome U133 Molecular Target: RNA Platform Description: 44,000 probeset 2-chip set [data repository] [Platform description]	Gene Logic (U Scherf, E Kaljian); Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH (W Reinhold)	Raw Data: cel files Processing method: GCRMA, MAS5, RMA 59 cell lines - LC:NCI_H23 is excluded
RNA: Affy HG-U95(A-E) [PMID:17339364]	Manufacturer: Affymetrix, Inc Platform: Human Genome U95 Molecular Target: RNA Platform Description: 65,000 probeset 5-chip set [data repository] [Platform description]	Gene Logic (U Scherf, D Dolginow); Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH (W Reinhold)	Raw Data: cel files (NCI60 only) Processing method: GCRMA, MAS5, RMA
RNA: ABC Transporters (RT-PCR) [PMID:15324696]	Manufacturer: NA Platform: RT_PCR Molecular Target: RNA Platform Description: 47 specific oligonucleotide probes were designed for each of the ABC transporters using DNAStar Primer Select. Expression levels were measured by real-time quantitative RT-PCR using the LightCycler RNA Amplification SYBR Green kit and a LightCycler machine. [data repository] [Platform description]	Laboratory of Cell Biology, CCR, NCI, NIH (M Gottesman, G Szakacs, J Ludwig); Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH	Raw Data: Crossing point values(log2) Processing method: Mean-centered, log2

Protein

Name	Platform Information	Principal Collaborators	Data Description
Protein: Antibody Array DTB [PMID:14623978]	Manufacturer: NCI LMP Genomics and Bioinformatics Group (Nishizuka) Platform: Reverse-phase lysate arrays (RPLA) using antibodies described in AbMiner at http://discover.nci.nih.gov/abminer/. Molecular Target: Protein Platform Description: Reverse-phase lysate arrays (RPLA) for 162 antibodies for 94 genes. Each array included 64 lysates (60 cancer cells and 4 replicate control pools) in 10 serial two-fold dilutions. [data repository] [Platform description]	LP, CCR, NCI (L Liotta); CBER, FDA (E Petricoin); Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH	Raw Data: Proteins detected using the catalyzed signal amplification system as described previously (Nishizuka et al, PNAS, 2003). Processing method: Dose interpolation analysis done using the DI25 algorithm. described previously (Nishizuka et al, PNAS, 2003).
Protein: SWATH (Mass spectrometry) [PMID:25730263]	Manufacturer: SCIEX Platform: SCIEX TripleTOF 5600 System mass spectrometer Molecular Target: Protein Platform Description: Cell pellets were processed using pressure cycling technology (PCT) using the barocycler NEP2320. Each digested samples was SWATHed using SCIEX TripleTOF 5600 System mass spectrometer in duplicates. [data repository] [Platform description]	Institute of Molecular Systems Biology, ETH Zurich (Tiannan Guo, Ruedi Aebersold)	Raw Data: Processing method: log10 transformation of peak area for each peptide precursor. Only SwissProt proteins are included in this data set.
Protein: Histone Modification [PMID:33658503]	Manufacturer: DNA signal derived from H3K27ac and H3K4me3 ChIP-seq Platform: ChIP-seq Molecular Target: Protein Platform Description: Active promoter signal marked by H3K4me3. Peaks were identified using MACS2. Raw read counts for each peak in each cell line was calculated using BAMscale. For each gene, the peak with the strongest average signal in the promoter area in cell lines was assigned. Raw read counts were normalized using the TMM-FPKM (edgeR R package) method, followed by log2(TMM-FPKM + 1) transformation. Cell line replicates were combined by calculating the mean signal for each assigned peak. [data repository] [Platform description]	Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH (Lorinc Pongor)	Raw Data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE143653 Processing method: TMM-FPKM (log2) values
Protein: Cell surface [PMID:36221114]	Manufacturer: Miltenyi Biotec Platform: MACSQuant VYB Molecular Target: Protein Platform Description: See links below. [data repository] [Platform description]	Quantitative Biology Center (QBiC) and Biomedical Data Science, Dept. of Computer Science, University of T�bingen (Simon Heumos); Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital T�bingen (Sandra Dehn)	Raw Data: Processing method: Cell surface expression of the 332 receptors was measured via flow cytometry using the MACSQuant VYB Analyzer (Miltenyi Biotec). Flow cytometry data was analyzed with the FlowLogic (Miltenyi-Inivai) software to obtain the mean fluorescence intensity (MFI) values of each analyzed receptor. The MFI was transformed using log to the base 2 after adding 1 (to account for zeros)

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