GC-1spg testis-cell lentiMPRA of human and chimpanzee HAR orthologs
A Human Accelerated Region is a Leydig cell GLI2 Enhancer that Affects Male-Typical BehaviorA triplicate lentiviral MPRA tested human and chimpanzee orthologs of 714 human accelerated regions in the GC-1spg mouse testis somatic cell line. The paper normalized RNA barcode reads to DNA barcode reads and reported 38 species-biased HAR hits in Figure 1C; because no target count matrix was deposited, table.csv is a hit-level extraction from that figure joined to the referenced 714-HAR library design for sequence and coordinate context.
Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.
Perturbation & assay details
Basal / Untreated
Synthetic human and chimpanzee HAR ortholog fragments were cloned upstream of a minimal promoter driving GFP in a lentiviral enhancer reporter, with unique DNA barcodes. Pooled libraries infected GC-1spg cells; DNA barcode sequencing measured integration and RNA barcode sequencing measured normalized reporter expression. Infection and DNA/RNA isolation were performed in triplicate. Multiple fragments represented each HAR, and the maximum ratio-score fragment was selected separately within each replicate and species. Limma modeling compared species across replicates and Benjamini-Hochberg correction was applied.
Processed data
50 rows per page. Click a cell to inspect its full value.
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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 12 definitions
- har_id
- HAR identifier reported in Figure 1C.
- human_biased
- True when the paper reports increased activity for the human ortholog relative to chimpanzee; false when human activity decreased.
- effect_direction
- Direction of the reported human-versus-chimpanzee MPRA activity difference.
- figure_rank_within_direction
- Top-to-bottom rank within the corresponding human-increased or human-decreased list in Figure 1C; this is not an effect-size rank beyond the plotted order.
- paper_hit_threshold
- Threshold stated in the Figure 1 caption for the displayed hits.
- highlighted_in_paper
- True only for the red-highlighted 2xHAR.238 bar in Figure 1C.
- human_reference_library_coordinates_hg19
- Coordinate range encoded in the human entry of the referenced GSE110758 714-HAR design; reference-library context, not a target-study measurement.
- chimp_reference_library_coordinates_hg19
- Coordinate range encoded in the chimpanzee entry of the referenced GSE110758 714-HAR design; reference-library context, not a target-study measurement.
- human_reference_library_fragment_lengths_bp
- Encoded fragment length and source HAR length for the human reference-library entry, formatted as tested_fragment/source_length.
- chimp_reference_library_fragment_lengths_bp
- Encoded fragment length and source HAR length for the chimpanzee reference-library entry, formatted as tested_fragment/source_length.
- source_figure
- Paper figure from which the hit status and list rank were extracted.
- qc_status
- All rows passed the paper-reported Figure 1C display threshold.
Quality control
The paper's reported analysis used triplicate infections, RNA/DNA normalization, per-replicate maximum ratio-score fragment selection, limma species comparisons, and Benjamini-Hochberg FDR correction. Figure 1C retained hits meeting FDR < 0.05 and fold-change > 0.2. No barcode-level counts, replicate correlations, or source result table were deposited; the processed table consequently includes only the 38 paper-reported Figure 1C hits and applies no unreported numerical filter.
Curation notes
This is a 2021 bioRxiv preprint. Europe PMC records no supplemental file or deposited data resource for the preprint, and no target-specific GEO count matrix was found. The linked GSE110758 design is the referenced 714-HAR library context from the earlier Ryu et al. study, not the GC-1 measurement dataset. Exact ratio scores, fold changes, FDR values, barcode counts, and replicate-level values are unavailable; the table intentionally preserves categorical direction and figure order instead of inventing numeric estimates. The target paper's later luciferase, 4C-seq, CRISPR, mouse expression, and behavior assays are not separate MPRA experiments and are not included here.