Data Associated with "Adaptive sequence divergence created new neurodevelopmental enhancers in humans", Mangan et. al, Submitted 2022
BED format files containing the positions, names, and maximum divergence density of HAQERs are available on the following human genome assemblies:
The following bigWig format files are available for data visualization on the UCSC Genome Browser:
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.
Raw sequencing reads from the following STARR-seq sequencing runs are provided in FASTQ format
fastq. (59 GB compressed)
Analyzed seurat object
RDS (120 MB compressed)
We provide the following relevant Excel spreadsheets.
Related to figure 1, an annotated spreadsheet of HAQER elements.
Related to figure 1, HAQER significance calculation.
Related to figure 3, HAQER/HAR ChromHmm enrichment analysis.
Related to figure 3, HAQER enrichment for elements gained after rhesus split.
VCF format variants from the 1000 Genomes Project annotated with the ancestral state from our inferred Human-Chimpanzee Ancestor.
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.