Codebook Data Page v2

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).

The changes relative to v1 (the bioRxiv version) are as follows (see Excel document for details):

• We fixed several sample mislabelings by examining k-mer enrichments between replicate SELEX experiments, and by searching for the recoded gene synthesis constructs in ChIP-seq reads. We relabeled affected experiments and PWMs.
• Next, we revised the MAGIX pipeline to begin with a peak-calling process, rather than genomic bins, and a thresholds was applied on the count of unique reads per peak. Thus, the GHT-SELEX peak locations and scores are "jittered" relative to the original versions.
• Next, we recalculated the TOPs and CTOPs.

Follow the link to browse the results

• TF and Plasmid Metadata (.xlsx)

• Readme (.txt)
• Metadata (.xlsx)
• Reads: All Reads(large .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)
  • Triple-optimized: Peaks Triple Optimized(.tar.gz)
  • Triple optimized overlapped: Peaks Triple Overlap(.tar.gz)
• Summits:
  • Toronto: Toronto Peaks(.tar.gz)
  • GrecoBit: GrecoBit Peaks(.tar.gz)
  • McGill: McGill Peaks(.tar.gz)

• Readme (.txt)
• Metadata(.xlsx)
• Reads:
  • All Reads(large .tar.gz)
  • Per TFs
  • GHT Merged BigWigs(.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)
• ZScores: Z-scores(.tar.gz)
• EScores: E-scores(.tar.gz)
• 8-mer statistics: 8-mers(.tar.gz)
• QCReports Paired: QC reports paired(.zip)
• QCReports: QC reports(.tar.gz)

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

• Metadata(.xlsx)
• Reads (trimmed): (.tar.gz)
• BigWigs: (.tar.gz)

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