A computational pipeline for comparative ChIP
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A computational pipeline for comparative ChIP-seq analyses Anaïs F. Bardet1, Qiye He2, Julia Zeitlinger2,3#, Alexander Stark1# 1 Research Institute of Molecular Pathology (IMP), Vienna 2 Stowers Institute for Medical Research, Kansas City; 3 Department of Pathology, University of Kansas Medical School, Kansas City # Corresponding authors (jbz@stowers.org, stark@starklab.org) Lab homepages: http://www.starklab.org, http://research.stowersinstitute.org/zeitlingerlab/ 1 Table S1: Performance of coordinate translation in vertebrates Schmidt et al.1 Mapped reads Translated reads CEBPA Mouse to Human 6938464 44% 3792526 55% CEBPA Dog to Human 6892619 47% 5368885 78% CEBPA Opossum to Human 3051354 72% 632429 21% CEBPA Chicken to Human 6631164 61% 630219 9% Kunarso et al.2 Mapped reads Translated reads CTCF Mouse to human 3686056 1947048 53% NANOG Mouse to human 8424102 4383803 52% OCT4 Mouse to human 4911144 2553512 52% Mikkelsen et al.3 Mapped reads Translated reads CTCF Mouse to human 8417901 4164699 49% PPARī§ Mouse to human 9887007 4240753 43% 2 Drosophila species D. melanogaster dm3 D. melanogaster (shorter reads) D. simulans droSim1 D. yakuba droYak2 D. erecta droEre2 D. ananassae droAna3 D. pseudoobscura dp4 Potential reads Table S2: Read mapping sensitivity for Drosophila species Mapped reads (%) 90.19 85.17 90.25 94.17 80.74 63.01 84.67 Genome coverage (%) 91.47 89.93 91.07 95.60 83.38 68.67 87.55 Percent of all potential 36 nucleotide long reads that can be uniquely mapped back to the genome and corresponding genome coverage. 3 Mapped reads Potential reads dp4 to dm3 D. pseudoobscura droAna3 to dm3 D. ananassae droEre2 to dm3 D. erecta droYak2 to dm3 D. yakuba to D. melanogaster droSim1 to dm3 Drosophila species D. simulans Table S3: Read translation sensitivity for Drosophila species Translated reads (%) 87.74 88.56 79.65 56.26 56.64 Genome coverage (%) 95.82 97.39 84.50 51.83 64.29 Translated reads (%) 95.85 95.87 89.30 70.47 61.33 Genome coverage (%) 95.29 76.48 82.25 50.28 62.31 Percent of all potential 36 nucleotide long reads or previously mapped reads (Table S2) that can be translated to the D. melanogaster genome and corresponding genome coverage. 4 REFERENCES 1. 2. 3. Schmidt, D. et al. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328, 1036–1040 (2010). Kunarso, G. et al. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet 42, 631–634 (2010). Mikkelsen, T.S. et al. Comparative Epigenomic Analysis of Murine and Human Adipogenesis. Cell 143, 156–169 (2010). 5
