Data

Data Associated with "Adaptive sequence divergence created new neurodevelopmental enhancers in humans", Mangan et. al, 2022

• BED format files containing the positions, names, and maximum divergence density of HAQERs are available on the following human genome assemblies:
  • hg38
  • T2T-CHM13_V2.0 Unmapped
  • hg19 Unmapped
The following bigWig format files are available for data visualization on the UCSC Genome Browser:
• HAQER Divergence Density (hg38)
• Related to figure 1, bigWig tracks for phylogenetic branch length metrics. Genomic regions where branch lengths were not evaluated are marked with a wig score of -10. Velocity Initial Velocity Acceleration
• Related to figures 3 and 5, bigWig tracks from developing human brain DHS-seq from the following three samples from the RoadMap epigenomic consortium: GSM595920(d117) GSM595922(d85) GSM595926(d96)
• Related to figure 1, the 5-way great ape alignment used for HAQER ascertainment. tgz (4.0 GB compressed)
• Related to figure 3 and 6, a bed of the search space for HAQERs, all ungapped regions larger than 1MB in hg38. BED (48kb)
• Raw sequencing reads from the following STARR-seq sequencing runs are provided in FASTQ format fastq. (59 GB compressed)
• Seurat workflow: Rscript
• Analyzed seurat object RDS (120 MB compressed)
• We provide the following relevant Excel spreadsheets.
  • Related to figure 1, an annotated spreadsheet of HAQER elements. xlsx
  • Related to figure 1, HAQER significance calculation. xlsx
  • Related to figure 3, HAQER/HAR ChromHmm enrichment analysis. xlsx
  • Related to figure 3, HAQER enrichment for elements gained after rhesus split. xlsx
• VCF format variants from the 1000 Genomes Project annotated with the ancestral state from our inferred Human-Chimpanzee Ancestor.
  • All 501 Unrelated African Individuals (1.9 GB compressed)
  • Esan
  • Gambian_Mandinka
  • Luhya
  • Mende
  • Yoruba
• Compressed project directories from my local machine tar.gz (963 MB compressed) and cluster tar.gz (23 GB compressed), which contain all relevant shell scripts for computational experiments and R scripts for data visualization.