Codebook Data Page v1

This page contains basic information about the Codebook data sets, including plasmid information, experiment metadata, processed data (peaks, etc) and PWMs. Please refer to publications for details. Raw data are found on SRA and GEO under PRJEB78913 (ChIP), PRJEB76622 (GHT-SELEX), PRJEB61115 (HT-SELEX), GSE275577 (PBM). .

Follow the link to browse the results

• TF and Plasmid Metadata (.xlsx)

• Readme (.txt)
• Metadata(.xlsx)
• Reads: All Reads(large .tar.gz)
• ChIP-seq mapped-reads (signal): ChIP Merged BedGraphs(.tar.gz)
• ChIP-seq BigWigs: ChIP Merged BigWigs(.tar.gz)
• Narrow Peaks:
  • Toronto: Toronto Peaks(.tar.gz)
  • GrecoBit: GrecoBit Peaks(.tar.gz)
  • McGill: McGill Peaks(.tar.gz)
  • Merged: Merged Peaks(.tar.gz)
• Summits:
  • Toronto: Toronto Peaks(.tar.gz)
  • GrecoBit: GrecoBit Peaks(.tar.gz)
  • McGill: McGill Peaks(.tar.gz)
  • Triple-optimized: Peaks Triple Optimized(.tar.gz)
  • Triple optimized overlapped: Peaks Triple Overlap(.tar.gz)

• Readme (.txt)
• Metadata(.xlsx)
• Reads:
  • All Reads(large .tar.gz)
  • Per TFs
  • GHT Merged BigWigs(.tar.gz)
  • GHT Merged BedGraphs(.tar.gz)
• BigWigs: BigWigs(large .tar.gz)
• Peaks:
  • Toronto: Narrow Peaks(.tar.gz)
  • Toronto: Summits(.tar.gz)
  • McGill: Magix Peaks(.tar.gz)
  • Triple-optimized: Peaks Triple Optimized(.tar.gz)
  • Triple optimized overlapped: Peaks Triple Overlap(.tar.gz)

• Metadata(.xlsx)
• Raw: Raw data(.tar.gz)
• 8-mer statistics: 8-mers(.tar.gz)
• QCReports: QC reports(.zip)

• Readme (.txt)
• Metadata(.xlsx)
• Raw: All Raw data(.tar.gz)

• All PWMs: Top 20 PWMs(.tar.gz)
• Expert_curated_PWMs_Hugheslab: Expert curated PWMs Hugheslab(.zip)
• Motif scans by MOODS: MOODS Triple Optimized(.tar.gz)
• TOPs: MOODS Triple-Optimized-Overlap (i.e., the intersection of MOODS Triple Optimized, ChIP-seq Triple Optimized, and GHT-SELEX Triple Optimized sets.) TOPs(.tar.gz)
• CTOPs: Conserved TOPs CTOPs(.tar.gz)

• Genome Browser tracks: Ancillary data(.tar.gz)

• Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors (bioRxiv)
• GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors (bioRxiv)
• Extensive binding of uncharacterized human transcription factors to genomic dark matter (bioRxiv)