DOI: 10.6084/m9.figshare.3420907
title: Project Achilles Copy Number Paper

description: Data deposit for the publication:Aguirre & Meyers, et al. Genomic copy number dictates a gene-independent cell response to CRISPR-Cas9 targeting. Cancer Discovery, 2016.<br>ABSTRACT: The CRISPR-Cas9 system enables genome editing and somatic cell genetic screens in mammalian cells. We performed genome scale loss-of-function screens in 33 cancer cell lines to identify genes essential for proliferation/survival and found a strong correlation between increased gene copy number and decreased cell viability after genome editing. Within regions of copy number gain, CRISPR-Cas9 targeting of both expressed and unexpressed genes, as well as intergenic loci, led to significantly decreased cell proliferation through induction of a G2 cell cycle arrest. By examining single guide RNAs that map to multiple genomic sites, we found that this cell response to CRISPR-Cas9 editing correlated strongly with the number of target loci. These observations indicate that genome targeting by CRISPR-Cas9 elicits a geneindependent anti-proliferative cell response. This effect has important practical implications for interpretation of CRISPR-Cas9 screening data and confounds the use of this technology for identification of essential genes in amplified regions.<br>--------------------------------------------<br>GeCKOv2 Achilles dataset33 cell lines<br>Achilles_v3.3.8_rawreadcounts.gct contains the raw read counts for each replicate, including a column containing read counts for initial pDNA library representation.<br>Achilles_v3.3.8_lognorm.gct contains the replicate-level read counts per million<br>Achilles_v3.3.8a.gct is the guide-level log2FC data used for analyses in the publication. It is not normalized across cell lines, but the median of the negative control sgRNAs are subtracted in each sample (i.e. a score of 0 represents median of the negative controls).<br>Achilles_v3.3.8.gct is guide-level log2FC data, that has been z-score normalized per replicate and has had sgRNAs targeting more than one genomic perfect match site removed. This data was used to calculate gene-level essentiality.<br>Achilles_v3.3.8_gene-soln.gct is the version of the data used for gene-level analyses across cell lines in the publication. Samples are z-score normalized and sgRNAs with &gt;1 perfect match are removed. Gene solutions computed using ATARiS.<br>Achilles_v3.3.8_ABSOLUTE_CN_segtab.txt contains the ABSOLUTE copy number segments for each of the 33 samples.<br>Achilles_v3.3.8_sgRNA_mappings.txt contains the mapped genomic locus (loci) for each sgRNA.<br><br><br>Analysis steps v3.3.8a:<br>1. QC and identify reps with reproducibility &lt;0.8 or are outliers on PCA or fail FP2. remove sgRNAs(guides) with low counts in DNA samples:completely remove shRNAs with median &lt;=1 3. remove replicates that fail QC measures 4. fold change(FC) with DNA pool samples 5. zero-center median of negative controls6. collapse replicates per line 7. sgRNAs are mapped to genes using(Achilles_v3.3.8a.gct)<br>Analysis steps v3.3.8:<br>1. QC and identify reps with reproducibility &lt;0.8 or are outliers on PCA or fail FP2. remove sgRNAs(guides) with low counts in DNA samples:completely remove shRNAs with median &lt;=1 3. remove sgRNAs(guides) that have &gt;1 perfect match anywhere in the reference genome 4. remove replicates that fail QC measures 5. fold change(FC) with DNA pool samples 6. Z score normalize each cell line7. collapse replicates per line 8. sgRNAs are mapped to genes (Achilles_v3.3.8.gct)9. ATARiS (pval=0.05) was run on guide-level data (Achilles_v3.3.8_gene-soln.gct)<br><br><br>NOTE: There was a minor error in an earlier version (3.3.7) of the data posted on figshare. Please use this one.<br><br>