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5 studies, 19 datasets.

Achilles Phase 2 (296.8MB)

Phase 2 of the Achilles pooled RNAi study: 'Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer', PNAS 2011 Jul 26;108(30):12372-7. Also available at www.broadinstitute.org/achilles

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

Annotations for the cell lines and shRNAs

TRChuV2.chip 3.5MB 12-Sep-2012 02:08:30 shRNA to gene annotation file for 54K library (older version)
non_overlapping_hairpins_cutoff_3.txt 2.7MB 12-Sep-2012 02:08:30 List of non-overlapping shRNAs (shRNAs with an offset of less than 3 basepairs)
55K_library_02152011.chip 3.6MB 12-Sep-2012 02:08:30 shRNA to gene annotation file for 54K library (newer version)
Paper_sampleannotation.txt 13.2KB 12-Sep-2012 02:08:30 Cell line annotation file, includes basic information including some mutation status data
Paper_arrayannotation.txt 34.2KB 12-Sep-2012 02:08:30 Annotation file by array (.CEL file)

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.

20110303_achilles2_PMAD_adjFC.rnai.gct 97.4MB 12-Sep-2012 02:08:37 File of normalized, shRNA adjusted log fold change values per cell line. Click 'Analyses' button to open directly in the GENE-E software. Or download to perform a class comparison using the GP modules 'MakeSubsetGctandCls' and 'ScoreByClassComp'.
20110303_achilles2.gct 122.3MB 12-Sep-2012 02:08:34 dCHIP array normalized file of shRNA values per replicate.
GENE-E_format.Ovarian.rnai.gct 1.6MB 12-Sep-2012 02:08:35 shRNA differential essentiality scores for a comparison of Ovarian cell lines vs all other lineages. Compatible with GENE-E software.
GENE-E_format.Colon.rnai.gct 1.6MB 12-Sep-2012 02:08:34 shRNA differential essentiality scores for a comparison of Colon cell lines vs all other lineages. Compatible with GENE-E software.
GENE-E_format.Pancreas.rnai.gct 1.6MB 12-Sep-2012 02:08:37 shRNA differential essentiality scores for a comparison of Pancreas cell lines vs all other lineages. Compatible with GENE-E software.
GENE-E_format.NSCLC.rnai.gct 1.6MB 12-Sep-2012 02:08:34 shRNA differential essentiality scores for a comparison of NSCLC cell lines vs all other lineages. Compatible with GENE-E software.
GENE-E_format.EsophagealSq.rnai.gct 1.6MB 12-Sep-2012 02:08:35 shRNA differential essentiality scores for a comparison of Esophageal Squamous cell lines vs all other lineages. Compatible with GENE-E software.
GENE-E_format.GBM.rnai.gct 1.6MB 12-Sep-2012 02:08:34 shRNA differential essentiality scores for a comparison of GBM cell lines vs all other lineages. Compatible with GENE-E software.
GENE-E_format.BRAF_Colon.rnai.gct 1.6MB 12-Sep-2012 02:08:35 shRNA differential essentiality scores for a comparison of BRAF mutant Colon cell lines vs wildtype BRAF Colon lines. Compatible with GENE-E software.
GENE-E_format.KRAS.rnai.gct 1.6MB 12-Sep-2012 02:08:37 shRNA differential essentiality scores for a comparison of KRAS mutant cell lines vs wildtype KRAS lines. Compatible with GENE-E software.
GENE-E_format.BRAF.rnai.gct 1.6MB 12-Sep-2012 02:08:34 shRNA differential essentiality scores for a comparison of BRAF mutant cell lines vs wildtype BRAF lines. Compatible with GENE-E software.
GENE-E_format.PIK3CA.rnai.gct 1.6MB 12-Sep-2012 02:08:35 shRNA differential essentiality scores for a comparison of PIK3CA mutant cell lines vs wildtype PIK3CA lines. Compatible with GENE-E software
Paper arrays.xls 18.0KB 12-Sep-2012 02:08:34 List of arrays processed by dCHIP

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

GP modules for Achilles 2 data analysis

RNAiGCTConverter.zip 1.7KB 12-Sep-2012 02:08:30 Converts file from dCHIP (array normalization steps) into a .gct file format for downstream analysis.
MakeArrayInfo.zip 44.6KB 12-Sep-2012 02:08:31 Makes an information file for each replicate array, using the cell line information (sample information file). The output is used to collapse replicate arrays to a single cell line in downstream steps and can be used as an sample annotation file in GENE-E when looking at data from individual replicates.
MvAplots.zip 10.5MB 12-Sep-2012 02:08:31 QC step; makes MvA plots of cell line replicate array data to look for replicate outliers.
shRNAscores.zip 10.6MB 12-Sep-2012 02:08:31 Collapses replicate sample data per cell line, calculates a fold change score compared to the reference (initial DNA plasmid pool).
MakeSubsetGctAndCls.zip 62.0KB 12-Sep-2012 02:08:31 Makes a .cls file and corresponding .gct dataset file for a class comparison of interest.
NormalizeCellLines.zip 795.3KB 12-Sep-2012 02:08:30 Normalizes cell line data by PMAD (or ZMAD).
ScorebyClassComp.zip 10.6MB 12-Sep-2012 02:08:30 Scores a class comparison of interest, results are compatible with GENE-E software.
Analysis_paper_schematic.pdf 46.6KB 12-Sep-2012 02:08:31 Figure showing analysis pipeline.

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/

UtilizingAchillesPhase2Datasets.doc 56.5KB 12-Sep-2012 02:08:30

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_102lines_gene_solutions.gct 15.0MB 19-Feb-2013 16:19:44 ATARiS gene solutions of 102 lines used in the PNAS 2011 paper.
Achilles_102lines_shRNA_table.txt 3.2MB 19-Feb-2013 16:20:30

Achilles Phase I (1.1MB)

Broad project Achilles phase 1 RNAi data

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).

AchillesData19celllines.txt 1.1MB 12-Sep-2012 02:21:26

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

Data from the 2008 paper "Modeling genomic diversity and tumor dependency in malignant melanoma", William M. Lin et al, Cancer Research, 2007. This dataset was previously available on the Broad Melanoma Portal.

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.

lin_et_al._sample_information_file_for_129_samples.xls 62.0KB 07-Nov-2012 11:38:22 Sample information file for all melanoma samples described in Lin et al.: Sample Name, Type, Platform (250K, 50K, HT-HGU133A), Provider, Well Location on GE plate, Array Name, Mutation status (BRAF, NRAS, PTEN, Other), CI-1040 GI50.
sampleinformationfile_874_forgistic.txt 90.0KB 07-Nov-2012 11:38:38 Sample information file for all the melanoma samples run on SNP arrays in addition to a collection of normal samples used for determination of copy number.

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.

Linetal.Figure2.pdf 408.5KB 07-Nov-2012 11:40:07 Figure 2. Clustering analysis of significant melanoma genomic alterations. Hierarchical clustering of GISTIC lesions (discretized smoothed copy number; see Materials and Methods) by the Euclidean distance metric and complete linkage.
linetal.table1and2.pdf 81.9KB 07-Nov-2012 11:40:24 Significant regions of chromosomal copy number alterations

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.

HTHGU133A_CELFILES.zip 239.3MB 07-Nov-2012 11:44:23 88 melanoma samples 5 normal melanocytes 1 breast cancer sample control
88MelanomaGeneExpression.txt 22.8MB 07-Nov-2012 11:45:16 88 RMA-normalized melanoma samples used in differential expression analyses

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

CopyNumber_101MelanomaSamples_250KStyIand50KXbaI_hg17_2.1.08.snp 301.0MB 07-Nov-2012 11:49:49 Copy number data for 101 melanoma samples processed as described in Lin et al. Basic steps: Batch correction, copy number calculation, per sample quality control, smoothing of copy number, combination of 250K and 50K data.
50KXbaSamples.tar 827.9MB 07-Nov-2012 12:18:33 Melanoma Short Term Culture and Cell Line and Normal samples (100 CEL files).
773CelFiles_a.zip 3.8GB 07-Nov-2012 13:46:59 Melanoma Short Term Culture and Normal samples (773 CEL files split across 5 zip file archives)
773CelFiles_b.zip 3.8GB 07-Nov-2012 13:52:43 Melanoma Short Term Culture and Normal samples (773 CEL files split across 5 zip file archives)
773CelFiles_c.zip 3.8GB 07-Nov-2012 14:02:18 Melanoma Short Term Culture and Normal samples (773 CEL files split across 5 zip file archives)
773CelFiles_d.zip 3.7GB 07-Nov-2012 14:05:36 Melanoma Short Term Culture and Normal samples (773 CEL files split across 5 zip file archives)
773CelFiles_e.zip 3.8GB 07-Nov-2012 14:10:56 Melanoma Short Term Culture and Normal samples (773 CEL files split across 5 zip file archives)

TCGA GBM and Ovarian (226.8MB)

GBM and Ovarian data from the TCGA project.

Gene Expression  (177.9MB) Gene expression  (Published) 

Gene Expression data from Affy U133aplus2

gbm_batch1-8_level3_exp.txt.recentered.normalized.080820.gct 47.9MB 12-Sep-2012 02:18:25
GBM_batch1-8_level3_exp.txt.recentered.normalized.080820.gct.tdf 130.0MB 12-Sep-2012 02:18:28

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

Segmented copy number data

broad.080528.seg.txt 35.3MB 12-Sep-2012 02:18:29

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

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

all_lesions_file.cap_regions.txt 59.8KB 12-Sep-2012 02:18:30
tcga-gbm-rae-genemap-n216-20080510-dscrt.txt 11.3MB 12-Sep-2012 02:18:30

Methylation  (1.9MB) Undefined  (Undefined) 

IGV Formatted methylation data

sorted.methylation.affy.080819.igv.txt 1.9MB 12-Sep-2012 02:18:30

Mutation  (111.8KB) Mutation  (In process) 

Mutation data (TCGA MAF format) summarized across multiple centers

cbrennan.maf 111.8KB 12-Sep-2012 02:18:29

Sample Annotation  (281.3KB) Sample annotation  (Unprocessed) 

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

public_igv_tcga_sample_info_20080807.txt 281.3KB 12-Sep-2012 02:18:29

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

The control of RNA alternative splicing is critical for generating biological diversity. Despite emerging genome-wide technologies to study RNA complexity, reliable and comprehensive RNA-regulatory networks have not been defined. Here, we used Bayesian networks to probabilistically model diverse data sets and predict the target networks of specific regulators. We applied this strategy to identify ~700 alternative splicing events directly regulated by the neuron-specific factor Nova in the mouse brain, integrating RNA-binding data, splicing microarray data, Nova-binding motifs, and evolutionary signatures. The resulting integrative network revealed combinatorial regulation by Nova and the neuronal splicing factor Fox, interplay between phosphorylation and splicing, and potential links to neurologic disease.

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.

1191150_dataset_S1.zip 39.8MB 12-Sep-2012 02:08:29
dataset_S1_Nova_CLIP_unique_tag_mm9.sort.bed 170.3MB 12-Sep-2012 02:08:28
dataset_S1_Nova_CLIP_unique_tag_mm9.sort.bed.idx 1.3MB 12-Sep-2012 02:08:29

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.

1191150_dataset_S2.zip 3.5MB 12-Sep-2012 02:08:30
dataset_S2_Nova_CLIP_cluster_mm9.sort.bed 13.6MB 12-Sep-2012 02:08:30
dataset_S2_Nova_CLIP_cluster_mm9.sort.bed.idx 1.3MB 12-Sep-2012 02:08:29

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.

1191150_dataset_S3.zip 10.6KB 12-Sep-2012 02:08:30
dataset_S3_Nova_target_cassette_nonredundant.mm9.sort.bed 27.9KB 12-Sep-2012 02:08:30