Achilles Phase 2 (296.8MB)

Achilles 2 Annotation files  (9.8MB) Sample annotation  (Published) 

Annotations for the cell lines and shRNAs

Achilles 2 RNAi Enrichment - 3/03/2011  (236.0MB) RNAi enrichment  (Published) 

Achilles RNAi dataset from the publication: 'Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer', PNAS 2011 Jul 26;108(30):12372-7.

Achilles 2 GenePattern modules  (32.7MB) Undefined  (Published) 

GP modules for Achilles 2 data analysis

Achilles 2 tutorials  (56.5KB) Undefined  (In process) 

Help for getting started with Achilles 2 pooled shRNA data. Also check: http://www.broadinstitute.org/cancer/software/GENE-E/

ATARiS  (18.2MB) RNAi enrichment  (Published) 

ATARiS analysis of the Achilles RNAi dataset (102 cell lines from the PNAS 2011 publication). See "ATARiS: Computational quantification of gene suppression phenotypes from multi-sample RNAi screens", Genome Research 2012 Dec 26 (Epub) and http://broadinstitute.org/ataris for details.

Achilles Phase I (1.1MB)

Cell Line Data  (1.1MB) RNAi  (Published) 

Raw cell viability data for each shRNA was generated 6 days post-infection in 384-well plates using an ATP-based luminescence assay (Cell-Titer Glo, Promega), with the exception of A549 cells, for which cell number was quantified using high throughput imaging. All wells were tested in quadruplicate, including duplicate samples with or without puromycin to assess infection efficiency. Data for shRNAs that yielded low infection efficiency (ie puromycin positive to puromycin negative ratio < 0.25) were excluded ('NT'). Data normalization was performed using the B-score metric, a variant of the Z-score that uses the median absolute deviation to account for plate-to-plate variability, as well as a two-way median polish to minimize row/column effects that accompany RNAi screens. The average of B-scores for all replicates (puromycin positive and negative) was calculated for each individual shRNA and aligned for the 5002 shRNAs (rows) tested across all 19 cell lines (columns).

Modeling genomic diversity and tumor dependency in malignant melanoma (20.4GB)

Sample Information Files  (152.0KB) Sample annotation  (Published) 

Sample information files for all the SNP array and gene expression samples included. Please note that the following files contain data from patient samples. The data should be treated confidentially and used purely for research purposes.

Tables and Figures   (490.4KB) Undefined  (Published) 

The most recent versions of the tables and figures, reflecting updated versions of the genome build (hg17) and the latest analytical processing algorithms.

Gene Expression Data  (262.2MB) Gene expression  (Published) 

Affymetrix HT-HGU133A gene expression data from melanoma short term cultures, melanoma cell lines, and normal samples. NOTE: The following data is derived from patient samples and should be treated confidentially and used only for research purposes.

SNP array data  (20.1GB) Affy SNP  (Published) 

Affymetrix 250K StyI and XbaI SNP array data from melanoma short term cultures, melanoma cell lines and normal samples. NOTE: The following data is derived from patient samples and should be treated confidentially and used only for research purposes

TCGA GBM and Ovarian (226.8MB)

Gene Expression  (177.9MB) Gene expression  (Published) 

Gene Expression data from Affy U133aplus2

Copy Number(Segmented)  (35.3MB) Agilent aCGH  (Published) 

Segmented copy number data

Copy Number (level 4)  (11.4MB) Agilent aCGH  (In process) 

TCGA level 4 processed and summarized copy number results including gistic and RAE results

Methylation  (1.9MB) Undefined  (Undefined) 

IGV Formatted methylation data

Mutation  (111.8KB) Mutation  (In process) 

Mutation data (TCGA MAF format) summarized across multiple centers

Sample Annotation  (281.3KB) Sample annotation  (Unprocessed) 

Sample annotation and linking identifiers for TCGA samples across the multiple data sets

The Nova Splicing-Regulatory Network and Its Combinatorial Controls (229.6MB)

Dataset S1  (211.3MB) Resequencing  (Published) 

Unique Nova CLIP tags. The coordinate of each tag mapped to the mouse genome (mm9) is shown in the BED format.

Dataset S2  (18.3MB) Resequencing  (Published) 

Nova CLIP tag clusters. The coordinate of each cluster in the mouse genome (mm9) is shown in the BED format. The peak height (PH) of each cluster is indicated in the score (5th) column.

Dataset S3  (38.5KB) Resequencing  (Published) 

325 non-redundant Nova target cassette exons. The coordinates of the cassette exon and flanking exons in the mouse genome (mm9) are shown in the BED format. Exons with Nova-dependent inclusion and exclusion are indicated by 1 and -1 in the score (5th) column, respectively.