CellMiner - Datasets

Data Set Metadata

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

Name	Platform Information	Principal Collaborators	Data Description
DNA fingerprinting	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.	Genomics and Bioinf Gp, LMP, CCR, NCI (P Lorenzi, S Varma, W Reinhold)	Raw Data:
DNA
DNA: aCGH Agilent 44k [citation]	Manufacturer: Agilent Technologies, Inc. Platform: Human Genome CGH Microarray 44A and 44B Molecular Target: DNA Platform Description: A genome-wide DNA copy number variation profiliny array containing 43,000 plus human sequences from both coding and non-coding regions. [Platform description]	Genomics and Bioinf Gp, LMP, CCR, NCI (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) Normalization method: Agilent Feature Extraction done with software version 8.1 with default settings for CGH arrays.
DNA: BAC aCGH [citation]	Manufacturer: University of California San Francisco Platform: BAC Clone arrays Molecular Target: DNA Platform Description: DNA samples from tumor cells and from normal controls were labeled with CY3 and CY5, respectively and hybridized to array comprised of 353 unique loci on the bacterial artificial chromosome microarray [data repository] [Platform description]	UCSF Comp Cancer Ctr(J Gray); Genomics and Bioinf Gp, LMP, CCR, NCI	Raw Data: ratio of sample vs control of DNA copy number Normalization method:
DNA: E-cadherin Methylation [citation]	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.	Gene Logic (D Dolginow), SAIC (D Munroe), Johns Hopkins Univ. (A Feinberg); Genomics and Bioinf Gp, LMP, CCR, NCI (W Reinhold)	Raw Data: sequence tracings Normalization 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: Roche NimbleGen 385k aCGH [citation]	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 Bioinf Gp, LMP, CCR, NCI	Raw Data: PAIR files Normalization method: Subtracted estimate of probe bias for each probe. A detailed explanation of the probe bias calculation is included with the normalized download. 59 cell lines - CO:HT29 is excluded
DNA: Sequencing [citation]	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. [Platform description]	Wellcome Trust Sanger Institute (M Stratton); Genomics and Bioinf Gp, LMP, CCR, NCI	Raw Data: NA Base-calling method: Mutation surveyor, Chromas, in-house Sanger software
RNA
RNA: ABC Transporters (RT-PCR) [citation]	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.	LCB, CCR, NCI (M Gottesman, G Szakacs, J Ludwig); Genomics and Bioinf Gp, LMP, CCR, NCI	Raw Data: Crossing point values(log2) Normalization method: Mean-centered
RNA: Affy HG-U95(A-E) [citation]	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 Bioinf Gp, LMP, CCR, NCI (W Reinhold)	Raw Data: cel files (NCI60 only) Normalization method: GCRMA, MAS5, RMA
RNA: Affy HG-U133(A,B) [citation]	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 Bioinf Gp, LMP, CCR, NCI (W Reinhold)	Raw Data: cel files Normalization method: GCRMA, MAS5, RMA 59 cell lines - LC:NCI_H23 is excluded
RNA: Affy HG-U133 Plus 2.0 [citation]	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. [Platform description]	Genomics and Bioinf Gp, LMP, CCR, NCI (W Reinhold)	Raw Data: cel files Normalization method: GCRMA, RMA 59 cell lines - ME:MDA_N is excluded
RNA: Affy HuEx 1.0 [citation]	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]	Bioinf Gp, LMP, CCR, NCI (W Reinhold); Affymetrix (T Gingeras); GeneLogic (E Kaldjian); MD Anderson (J Weinstein)	Raw Data: cel files Normalization method: GCRMA
RNA: Agilent mRNA [citation]	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 Bioinf Gp, LMP, CCR, NCI (W Reinhold)	Raw Data: Text files with data and PDF files with quality information Normalization method: Processed using GeneSpring
RNA: Agilent Human miRNA (V2) [citation]	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.	Agilent Technologies (S Fulmer-Smentek, P D'Andrade); Genomics and Bioinf Gp, LMP, CCR, NCI	Raw Data: Data in tab delimited text files. Array quality information as PDF files Normalization method:
RNA: miRNA OSU V3 chip [citation]	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 Bioinf Gp, LMP, CCR, NCI	Raw Data: Two channel sample and background intensity measurements. Normalization method: From the Genepix data, we selected human probes (entries with ID=hsa-[anything]) and median signal intensity minus background for each spot (column labeled 'F635 Median - B635'). After converting any negative values to 1, signal intensities were log2-transformed, and duplicate spots were averaged. Then we performed quantile normalization across the 3 microarray batches, replaced all values less than 5 with the median of such values, and set the value for each control cell line to the mean of its five replicates.
RNA: OSU Transporter Array [citation]	Manufacturer: Ohio State University Platform: Spotted Array Molecular Target: RNA Platform Description: Spotted 70-mer microarray	OSU (W Sadee); Genomics and Bioinf Gp, LMP, CCR, NCI	Raw Data: Normalization method: Normalization based on robust, locally linear fits (Loess), implemented in the SMA R package
Protein
Protein: Lysate Array [citation]	Manufacturer: NCI LMP Genomics and Bioinformatics Group (Nishizuka) Platform: Reverse-phase lysate arrays (RPLA) Molecular Target: Protein Platform Description: Reverse-phase lysate arrays (RPLA) for 176 antibodies. Each array included 64 lysates (60 cancer cells and 4 replicate control pools) in 10 serial two-fold dilutions. [data repository]	LP, CCR, NCI (L Liotta); CBER, FDA (E Petricoin); Genomics and Bioinf Gp, LMP, CCR, NCI	Raw Data: Signal intensity processed by DI25 algorithm (log2) Normalization method: DI25 optimization
Drug
Drug: A118 [citation]	Manufacturer: Developmental Therapeutics Program, NCI/NIH Platform: Sulforhodamine assay Molecular Target: Platform Description: Negative log10(Gi50) values of Sulforhodamine assay for 118 molecules (also known as the Standard Agents) with known 2D structure, known mechanism of action and have been tested at-least 4 times. Higher values equate to higher sensitivity of cell lines.	LMP, CCR, NCI (K Kohn); DPT, NCI (D Zaharevitz); Genomics and Bioinf Gp, LMP, CCR, NCI	Raw Data: Normalization method:
Drug: A1429 [citation]	Manufacturer: Developmental Therapeutics Program, NCI/NIH Platform: Sulforhodamine assay Molecular Target: Platform Description: Negative log10(Gi50) values of Sulforhodamine assay for 1429 molecules (also known as the Standard Agents) with known 2D structure, known mechanism of action for many of the drugs and have been tested at-least 4 times. Higher values equate to higher sensitivity of cell lines.	DPT, NCI (D Zaharevitz, S Bates); Genomics and Bioinf Gp, LMP, CCR, NCI	Raw Data: Normalization method:
Drug: A4463 [citation]	Manufacturer: Developmental Therapeutics Program, NCI/NIH Platform: Sulforhodamine assay Molecular Target: Platform Description: Negative log10(Gi50) values of Sulforhodamine assay for 4463 molecules (also known as the Standard Agents) with known 2D structure and have been tested at-least 2 times. Higher values equate to higher sensitivity of cell lines.	DPT, NCI (D Zaharevitz, S Bates); Genomics and Bioinf Gp, LMP, CCR, NCI	Raw Data: Normalization method:

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