Primer Sequences for MPRA Cloning of Archaic Human Variants

Primer sequences used in a massively parallel reporter assay (MPRA) to study the regulatory effects of 25,869 introgressed Neanderthal and Denisovan SNPs. The dataset, authored by Maddy Comerford, supports research into how archaic hominin DNA influences present-day human immune gene regulation. It is a small dataset (9.3 KB) provided in XLSX format.

Use Cases

• Design PCR primers targeting specific archaic SNP alleles listed in the sequence data for functional validation studies.
• Map primer sequences to genomic coordinates of the 25,869 introgressed SNPs to plan MPRA cloning experiments.
• Analyze primer sequences for potential off-target binding when studying immune genes like IFIH1 and TNFAIP3.

Strengths

• Focuses on a specific, high-confidence set of 25,869 introgressed SNPs from Neanderthal and Denisovan sources.
• Primer data is directly linked to a published MPRA study on archaic variant regulatory activity in immune cells.
• Released under a permissive CC BY 4.0 license, enabling reuse and modification.

Limitations

• Very small in scale (9.3 KB), containing only primer sequences without the associated assay results or variant annotations.
• Lacks explicit column definitions and sample data, making initial assessment of data structure difficult.
• Scope is limited to primer design for a specific study, not a general-purpose primer database.

Provenance

Source

Maddy Comerford via figshare.

Collection Method

Primer sequences designed for a massively parallel reporter assay (MPRA) investigating introgressed SNPs.

Freshness

Last updated March 24, 2026.

Geography

Associated with genetic studies in populations of Papuan genetic ancestry.