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• Tae Hoon Kim, Ziedulla K. Abdullaev, Andrew D. Smith, Keith A. Ching, Dmitri I. Loukinov, Roland D. Green, Michael Q. Zhang, Victor V. Lobanenkov and Bing Ren Analysis of the vertebrate insulator protein CTCF binding sites in the human genome
  

Supplementary Materials

• Supplementary text, figures, and tables (7.2 MB) PDF


• archive1.zip (98.2 MB)- primary data files, see manifest
  hg16 PCR arrays and hg17 condensed array data.


• genome.zip (520.6 MB)- primary data files, see manifest
  hg17 Genome wide array data.


• genomeDesignFiles.zip (746.7 MB)- primary data files, see manifest


• normalized_genome.zip (319.5 MB)- primary data files, see manifest

• ctcf.imr90.hg17.bed.zip (119.1 kB)
  hg17 BED file of 13804 CTCF coordinates from IMR90 cells
• ctcf.imr90.hg17.masked.fasta.zip (3.4 MB)
  repeat masked hg17 sequence fasta file of 13804 CTCF from IMR90 cells
• big.wig.gz (2.0 MB)
  Combined hg17 wig file for UCSC browser
• conservation.zip (103.9 kB)
  12799 ctcf sites conserved via 17way alignment (hg17).
• motif.zip (356.5 kB)
  31905 predicted 20-mer motifs (hg17).
• core.zip (27.0 kB)
  CTCF core motif in IMR90 without 20-mer motif (hg17).
Alternate download site and additional data.
• Nathaniel D. Heintzman, Rhona K. Stuart, Gary Hon, Yutao Fu, Christina W. Ching, R. David Hawkins, Leah O. Barrera, Sara Van Calcar, Chunxu Qu, Keith A. Ching, Wei Wang, Zhiping Weng, Roland D. Green, Gregory E. Crawford and Bing Ren Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

Supplementary Materials

• Supplementary_Text.doc (172K)
  Supplementary methods and legends for Supplementary figures and tables used in the manuscript. (Word)
• Supplementary_Figures.zip (5.3 Mb) manifest
  S ix Supplementary figures. (PDF)
• Supplementary_Tables.zip (310K) manifest
  Ten Su pplementary Tables. (Excel)

• Microarray_design_files.zip (42.0 Mb) manifest
  
o Design information for the microarray platforms used in these experiments.

• Microarray_processed_data.zip (151.5 Mb) m anifest
  - Normalized average data from replicate experiments.
  - Target lists generated using Mpeak and NimbleGen microarray data.
  
• Microarray_raw_data.zip (760.3 Mb) manifest
  - Unprocessed data from all experiments.
  
• DNase-chip_raw_data.zip (121.1 Mb) manifest
  - Unprocessed data from all DNase-chip experiments.
  
• DNase-chip_processed_data.zip (4.7 Mb) man ifest
  - Normalized average data from replicate DNase-chip experiments.
  - DHS list generated using ACME and NimbleGen microarray data.
  
• TRAP220_processed_data.zip (7.7 Mb) manifest
  - Normalized average data from replicate experiments.
  - Target list generated using Mpeak and NimbleGen microarray data.
  
• TRAP220_raw_data.zip (41.7 Mb) manifest
  - Unprocessed data from all experiments.
  
• HeLa_IFN_Affy.zip (9.6 Mb) Affymetrix CEL files of control and IFN-gamma stimulated HeLa cells
  

• SignalMap1_8.zip (4.2 Mb)

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• Tae Hoon Kim, Leah O. Barrera, Ming Zheng, Chunxu Qu, Michael A. Singer, Todd A. Richmond, Yingnian Wu, Roland D. Green and Bing Ren. A high-resolution map of active promoters in the human genome. Nature, 2005. Aug 11;436(7052):876-80. Epub 2005 Jun 29.
Supplemental Data:
• Mpeak program used for tiling array analysis
• Affymetrix IMR90 gene expression raw CEL data
• Gene expression data
• Condensed array data
• Novel promoter RNA hybridization data
• Processed data
• Supplementary Notes: The file contains Supplementary Methods and legends for Supplementary Figures and Supplementary Tables used in the paper
• Supplementary Figures S1-S6: The file contains six Supplemental Figures in order that accompany the manuscript. The legends for these figures are included in the Supplementary Notes.
• Supplementary Table S1: 9,328 TAF1 binding sites matched to known 5 ends.
• Supplementary Table S2: 1,239 putative promoters (Acembly-match and no 5 end match).
• Supplementary Table S3: Validation of putative promoters.
• Supplementary Table S4: Multiple promoter usage.
• Supplementary Table S5: Clusters of genes with TAF1-bound promoters.
• Supplementary Table S6: Gene expression classes.
• Supplementary Table S7: Histone modification on class III and IV genes.


• Kim TH, Barrera LO, Qu C, Van Calcar S, Trinklein ND, Cooper SJ, Luna RM, Glass CK, Rosenfeld MG, Myers RM, Ren B. Direct isolation and identification of promoters in the human genome. Genome Res. 2005 Jun;15(6):830-9. Epub 2005 May 17.
Supplemental data and raw data used in the analysis:
• Supp Material (MS Word)
• Supp Table 1 A-I (MS Excel)
• Supp Table 2 A-G (MS Excel)
• Supp Table 3 A-H (MS Excel)
• GPR files
• Average files


• Li, Z., Van Calcar, S., Qu, C., Cavenee, W.K., Zhang, M.Z., and Ren, B., A Global Transcriptional Regulatory Role for c-Myc in Burkitt's Lymphoma Cells. Proc. Natl. Acad. Sci., 2003; 100:8164-8169
Supplemental data and raw data used in the analysis:
• Supporting Array Description
• Supporting Materials and Methods
• Supporting Data Set for Figure 2
• Supporting Data Set for Figure 4
• GPR files
• Average files


• Nathaniel D. Maynard, Jing Chen, Rhona K. Stuart, Jian-Bing Fan, and Bing Ren. Genome-wide Mapping of Allele-specific Protein-DNA Interactions in Human Cells. Nature Methods, 2008; 5:307-309 .
Supplemental data and raw data used in the analysis:
• HumanHap300 Datasets for RNAP ChIP-SNP (includes data from genomic DNA, 3 inputs, and 3 RNAP ChIPs)
• Allele-Specific Expression Datasets for IMR90