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note
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Funding for this work came from the NHGRI of the NIH as part of the modENCODE project, NIH (grant R01GM088565), Muscular Dystrophy Association, and the Pew Charitable Trusts (J. K. K.); the Helmholtz-Alliance on Systems Biology (Max Delbrück Centrum Systems Biology Network) (S. D. M.); the Wellcome Trust (J. A.); the William H. Gates III Endowed Chair of Biomedical Sciences (R. H. W.); and the A. L. Williams Professorship (M. B. G.). M. Snyder has an advisory role with DNANexus, a DNA sequence storage and analysis company. Transfer of GFP-tagged fosmids requires a Materials Transfer Agreement with the Max Planck Institute of Molecular Cell Biology and Genetics. Raw microarray data are available from the Gene Expression Omnibus archive, and raw sequencing data are available from the SRA archive (accessions are in table S18). We appreciate help from S. Anthony, K. Bell, C. Davis, C. Dieterich, Y. Field, A. S. Hammonds, J. Jo, N. Kaplan, A. Manrai, B. Mathey-Prevot, R. McWhirter, S. Mohr, S. Von Stetina, J. Watson, K. Watkins, C. Xue, and Y. Zhang, and B. Carpenter. We thank C. Jan and D. Bartel for sharing data on poly (A) sites before publication, WormBase curator G. Williams for assistance in quality checking and preparing the transcriptomics data sets for publication, as well as his fellow curator P. Davis for reviewing and hand-checking the list of pseudogenes.
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