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1 studies, 6 datasets.

Cancer Cell Line Encyclopedia (55.6GB)

    

DNA Copy Number  (41.3GB) Affy SNP  (Published) 

Affymetrix SNP6.0 arrays.
Raw Affymetrix CEL files were converted to a single value for each probe set representing a SNP allele or a copy number probe. Copy numbers were then inferred based upon estimating probe set specific linear calibration curves, followed by normalization by the most similar HapMap normal samples. Segmentation of normalized log2 ratios (specifically, log2(CN/2)) was performed using the circular binary segmentation (CBS) algorithm.
CCLE_copynumber_byGene_2012-09-29.txt 151.4MB 17-Oct-2012 14:38:48 Copy-number values per gene. All genes from the TCTA hg19 GAF 2.1 Jun2011 reference transcripts were considered.
CCLE_SNP.Arrays.sif_2012-09-29.txt 142.4KB 17-Oct-2012 14:58:51 SNP-specific sample-info-file, with batch information.
CCLE_SNP.Birdseed.Calls_2012-09-29.tar.gz 4.1GB 17-Oct-2012 15:02:14 Genotype calls from Affymetrix genotyping arrays. These calls were created using Birdsuite.
CCLE_copynumber_2012-09-29.seg.gz 12.1MB 18-Oct-2012 23:45:34 Segmented copy-number profiles in the .seg Gzip-compressed format. (hg19)
CCLE_copynumber_2012-09-29.seg 41.4MB 18-Oct-2012 23:47:47 Segmented copy-number profiles in the .seg file format. (hg19)
CCLE_SNP.Arrays_2012-10-30_1.tar.gz 12.0GB 30-Oct-2012 13:55:38 Compressed archive of the raw CEL files -- Part 1
CCLE_SNP.Arrays_2012-10-30_2.tar.gz 11.9GB 30-Oct-2012 14:45:36 Compressed archive of the raw CEL files -- Part 2
CCLE_SNP.Arrays_2012-10-30_3.tar.gz 6.5GB 30-Oct-2012 16:12:12 Compressed archive of the raw CEL files -- Part 3
CCLE_SNP.Arrays_2012-10-30_4.tar.gz 6.6GB 30-Oct-2012 17:15:37 Compressed archive of the raw CEL files -- Part 4 (controls)

mRNA expression  (7.9GB) Gene expression  (Published) 

Affymetrix U133+2 arrays.
Raw Affymetrix CEL files were converted to a single value for each probe set using Robust Multi-array Average (RMA) and normalized using quantile normalization. Either the original Affymetrix U133+2 CDF file or a redefined custom CDF file (ENTREZG - v15) was used for the summarization.
CCLE_Expression_2012-09-29.res 589.6MB 17-Oct-2012 15:17:12 RMA-normalized mRNA expression data. (Affymetrix annotations)
CCLE_Expression_Entrez_2012-09-29.gct 167.2MB 17-Oct-2012 16:30:23 Gene-centric RMA-normalized mRNA expression data. (ENTREZG v15 CDF file, see the Brainarray website for more details about the probe set annotations; gct file format.
CCLE_Expression.Arrays.sif_2012-10-18.txt 124.6KB 18-Oct-2012 17:24:33 Expression arrays samples info file.
CCLE_Expression_Entrez_2012-10-18.res 204.6MB 18-Oct-2012 17:43:56 Gene-centric RMA-normalized mRNA expression data. (ENTREZG v15 CDF file, see the Brainarray website for more details about the probe set annotations; res file format)
CCLE_Expression_Entrez_IGV_2012-09-29.tdf 2.0GB 19-Oct-2012 12:54:42 Gene-centric RMA-normalized mRNA expression data (ENTREZG v15 CDF). This format is only meant to be used with the Integrative Genomics Viewer (IGV, available in the "Analysis tools" section) and the value for each probe set is median-centered and divided by the MAD (robust z-score).
CCLE_Expression.Arrays_2013-03-18.tar.gz 5.0GB 19-Mar-2013 16:12:37 Raw CEL files in a compressed archive.

Cell Line Annotations  (196.1KB) Sample annotation  (Published) 

CCLE_sample_info_file_2012-10-18.txt 196.1KB 18-Oct-2012 17:21:01 Cell line annotations

Oncomap mutations  (464.8KB) Mutation  (Published) 

Oncomap mutation data.
The mutations were assessed in 33 genes (381 specific mutations) using Oncomap 3.0 core. See the associated publication.
CCLE_Oncomap3_2012-04-09.maf 318.2KB 10-Apr-2012 09:14:09 List of mutations (hg18) in the Mutation Annotation Format (MAF). See the sample info file for the list of all cell lines tested on Oncomap.
CCLE_Oncomap3_Assays_2012-04-09.csv 146.7KB 10-Apr-2012 09:15:08 List of assays for Oncomap 3 (core). All these mutations were tested in all samples for which there are Oncomap results.

Hybrid capture sequencing  (6.4GB) Mutation  (In process) 

List of mutations and indels in 1651 genes, determined by targeted massively parallel sequencing. Note: the hybrid capture process might yield sequences in genes outside of the target list; those were kept in the analysis and mutations in these genes are present in the files below.
CCLE_hybrid_capture1650_HGNC_info_2012.02.20.txt 111.7KB 01-Mar-2012 15:51:10 HGNC information for the list of 1651 genes selected for hybrid capture/sequencing.
CCLE_hybrid_capture1650_hg19_NoCommonSNPs_NoNeutralVariants_CDS_2012.05.07.maf 56.5MB 22-May-2012 15:40:04 List of mutations across CCLE cell lines, in MAF format. Preferred dataset
The following variants were filtered out:
  • common polymorphisms,
  • allelic fraction < 10%,
  • putative neutral variants (missenses present in less than 2 warm-blooded vertebrates),
  • located outside of the CDS for all transcripts.
CCLE_hybrid_capture1650_hg19_NoCommonSNPs_CDS_2012.05.07.maf.gz 6.0MB 22-May-2012 15:44:02 List of mutations across CCLE cell lines, in MAF format.
The following variants were filtered out:
  • common polymorphisms,
  • allelic fraction < 10%,
CCLE_hybrid_capture1650_hg19_allVariants_2012.05.07.maf.gz 96.9MB 22-May-2012 15:44:59 List of variants across CCLE cell lines with an allelic fraction >10%, in MAF format.
CCLE_hybrid_capture1650_hg19_interval_lists.tar.gz 669.6KB 30-May-2012 14:44:11 Lists of targets and baits for the hybrid capture.
CCLE_hybrid_capture1650_hg19_coverage_2012.06.19.tar.gz 6.2GB 19-Jun-2012 17:16:33 Hybrid selection sequencing coverage per base, in the wig file format.
CCLE_hybrid_capture1650_hg19_NoCommonSNPs_NoNeutralVariants_CDS_2012.05.07.maf.gz 5.2MB 24-Oct-2012 07:40:38 List of mutations across CCLE cell lines, in MAF format. Preferred dataset
The following variants were filtered out:
  • common polymorphisms,
  • allelic fraction < 10%,
  • putative neutral variants (missenses present in less than 2 warm-blooded vertebrates),
  • located outside of the CDS for all transcripts.
GZipped for faster downloading.

Pharmacological profiling  (2.3MB) Drug data  (Published) 

Pharmacologic profiles for 24 anticancer drugs across 504 cell lines.
CCLE_NP24.2009_Drug_data_2012.02.20.csv 2.3MB 20-Jun-2012 14:52:21 Pharmacologic profiles for 24 anticancer drugs across 504 CCLE lines.
CCLE_NP24.2009_profiling_2012.02.20.csv 2.4KB 17-Apr-2012 13:03:02 List of the 24 drugs profiled across 504 CCLE lines.