SUPPLEMENTAL MATERIAL

DNA Replication Timing

• Schübeler D, Scalzo D, Kooperberg C, van Steensel B, Delrow J, Groudine M (2002) Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing.Nature Genet 32:438-442
  
  The file contains the ID of each listed gene (Rubin, G.M. et al. Science 287, 2222-2224 (2000)), which can be searched via flybase. The replication timing ratio(early over late) is provided in log2 scale for the raw and smoothed values (see Figure 2a of the manuscript for illustration). In addition the expression status of each gene is given (1=expressed, 0=not expressed, 8=undefined).
  Replication timing dataset
  


• Schwaiger M, Stadler M, Bell O, Kohler H, Oakeley E, Schübeler D (2009) Chromatin state marks cell-type and gender specific replication of the Drosophila genome. Genes Dev 23:589-601
  
  The zip file (~1 MB) contains the supplemental data files.
  Processed data files (in .zip folder)
  All microarray datasets can be downloaded from the GEO website:
  GEO: GSE13328
  The replication domains in the paper can be viewed online at
  replicationdomain.org
  


• Schübeler D, MacAlpine D, Scalzo D, Wirbelauer C, Kooperberg C, van Leeuwen F, Gottschling D, O'Neill L, Turner B, Delrow J, Bell SP, Groudine M (2004) The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev 18:1263-1271
  
  The complete array dataset can be downloaded as an excel or text (tab delimited) using the following links
  Chromatin 2004 (txt)
  Chromatin 2004 (xls)
  The files contain the average log² ratio for each modification, gene ID and genomic position.
  

Chromatin Structure

• Bell O, Conrad T, Kind J, Wirbelauer C, Akhtar A, Schübeler D (2008) Transcription-coupled methylation of histone H3 at lysine 36 regulates dosage compensation by enhancing recruitment of the MSL complex in Drosophila. Mol Cell Biol 28: 3401-3409
  
  Word file // PDF file
  


• Weber M, Davies J, Wittig D, Oakeley E, Haase M, Lam WL, Schübeler D (2005) Chromosome-wide and promoter-specific analyses reveal sites of differential DNA methylation in normal and transformed human cells.Nature Genet (37:853-862)
  
  Normalized complete datasets can be downloaded using the following links:
  CpG islands
  SMRT (BAC)
  Experimental datasets are available through GEO (accession numbers GSE2653 and GSE2664)
  

DNA Methylation

• Weber M, Hellmann I, Stadler MB, Ramos L, Pääbo S, Rebhan M, Schübeler D (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nature Genet (39, 457 - 466)
  
  The normalized promoter values can be downloaded using the following link:
  Promoter Set (xls)
  The complete experimental datasets are available through GEO (accession number GSE6715)
  


• Mohn F, Weber M, Rebhan M, Roloff TC, Richter J, Stadler MB, Bibel M, Schübeler D (2008) Lineage-Specific Polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Molecular Cell 30: 755-766
  
  The normalized promoter values can be downloaded using the following link:
  Promoter Set (txt)
  The complete experimental datasets are available through GEO (accession number GSE11489)