Experiment / E40SOUTOBIntegrated lentiMPRA

Modern-versus-archaic lentiMPRA in H1-derived neural progenitor cells

The cis-regulatory effects of modern human-specific variants

The study assayed 200-bp archaic/ancestral and modern/derived sequence pairs centered on fixed or nearly fixed modern-human-specific single-nucleotide variants in neural progenitor cells differentiated from H1 embryonic stem cells. Three independent lentiMPRA infections were quantified through barcode RNA/DNA abundance.

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Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CL:0011020
Reference genome: hg19
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Perturbation not reported.

Integrated lentiviral MPRA constructs carried the 200-bp candidate sequence pair, a minimal promoter, and transcribed barcode readouts in the reporter 5′ UTR. Barcode RNA and DNA abundance were measured in three replicates; MPRAnalyze estimated allele activity and modern-versus-archaic differential activity.

Processed data

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Column dictionary · 40 definitions

variant_id: Synthetic coordinate identifier in the form chromosome:central hg19 position; this study does not assign an rsID to these fixed modern-human-specific variants.
sequence_id: Study/library identifier for the 200-bp archaic/modern sequence pair.
chromosome: Chromosome containing the central tested variant.
central_variant_position_hg19: 1-based central variant coordinate on hg19.
central_variant_position_hg38: 1-based central variant coordinate on hg38.
oligo_start_hg19: 1-based start coordinate of the 200-bp oligo on hg19.
oligo_end_hg19: 1-based end coordinate of the 200-bp oligo on hg19.
oligo_start_hg38: 1-based start coordinate of the 200-bp oligo on hg38.
oligo_end_hg38: 1-based end coordinate of the 200-bp oligo on hg38.
n_variants_in_sequence: Number of modern-versus-archaic differences within the 200-bp sequence window.
archaic_allele: Base at the central variant position in the archaic/ancestral sequence.
modern_allele: Base at the central variant position in the modern/derived sequence.
archaic_sequence_200bp: 200-bp archaic/ancestral sequence tested in the lentiMPRA.
modern_sequence_200bp: 200-bp modern/derived sequence tested in the lentiMPRA.
closest_gene_symbol: HGNC symbol of the closest gene reported by the study.
linked_genes_stringent: Cell-type-specific stringent linked HGNC gene symbols from Supplementary file 1h, comma-separated.
chromhmm_state: Cell-type-specific ChromHMM state annotation from Supplementary file 1f.
archaic_rna_dna_ratio: Aggregated archaic barcode RNA abundance divided by DNA abundance for this cell type.
modern_rna_dna_ratio: Aggregated modern barcode RNA abundance divided by DNA abundance for this cell type.
archaic_dna_cpm: Archaic barcode DNA abundance in counts per million.
modern_dna_cpm: Modern barcode DNA abundance in counts per million.
archaic_rna_cpm: Archaic barcode RNA abundance in counts per million.
modern_rna_cpm: Modern barcode RNA abundance in counts per million.
log2_activity_ratio_modern_vs_archaic: Derived log2(modern RNA/DNA ratio divided by archaic RNA/DNA ratio); not the MPRAnalyze estimate.
archaic_activity_alpha: MPRAnalyze estimated transcription rate (alpha) for the archaic/ancestral allele.
archaic_activity_pvalue: MPRAnalyze MAD-score-based activity p-value for the archaic/ancestral allele.
archaic_activity_fdr: Benjamini-Hochberg FDR for archaic/ancestral allele activity; blank where not reported in the source.
modern_activity_alpha: MPRAnalyze estimated transcription rate (alpha) for the modern/derived allele.
modern_activity_pvalue: MPRAnalyze MAD-score-based activity p-value for the modern/derived allele.
modern_activity_fdr: Benjamini-Hochberg FDR for modern/derived allele activity; blank where not reported in the source.
archaic_barcode_count: Number of unique barcodes associated with the archaic/ancestral construct.
modern_barcode_count: Number of unique barcodes associated with the modern/derived construct.
differential_log2_fc_modern_vs_archaic: MPRAnalyze log2 fold-change of modern/derived activity relative to archaic/ancestral activity.
differential_pvalue: MPRAnalyze p-value for differential modern-versus-archaic activity.
differential_fdr: Benjamini-Hochberg FDR for differential activity among active sequence pairs; blank where not reported in the source.
active: Paper's final active-sequence call (Yes/No), based on MPRAnalyze activity plus the empirical scrambled-sequence RNA/DNA threshold.
differentially_active: Paper's final differential-activity call (Yes/No) at FDR <= 0.05 among active sequence pairs.
replicate1_log2_fc: Per-replicate log2 fold-change of modern/derived versus archaic/ancestral activity from Supplementary file 1j.
replicate2_log2_fc: Per-replicate log2 fold-change of modern/derived versus archaic/ancestral activity from Supplementary file 1j.
replicate3_log2_fc: Per-replicate log2 fold-change of modern/derived versus archaic/ancestral activity from Supplementary file 1j.

Quality control

The paper used MPRAnalyze with replicate-aware RNA/DNA models, required at least 10 barcodes for both alleles before calling activity, applied an empirical scrambled-sequence RNA/DNA FDR <= 0.05 after excluding scrambled sequences more than 2 standard deviations from their mean, and called modern-versus-archaic differential activity at Benjamini-Hochberg FDR <= 0.05 among active pairs. For this package, rows were additionally required to have complete coordinates, both 200-bp sequences, and complete core measurements; pairs with fewer than 10 barcodes for either allele or missing core measurements were excluded. The table retains both active and inactive QC-passing pairs: 13607 of 14,042 source pairs retained (431 removed for low barcode coverage; 4 removed for missing core measurements); 602 are paper-called active and 153 are paper-called differentially active.

Curation notes

The source calls the non-modern sequence “archaic”; it is the ancestral allele used as the modern-human comparison. These are genome-wide fixed or nearly fixed modern-human-specific variants rather than dbSNP-tagged common variants, so variant_id is a coordinate identifier and not an rsID. The 200-bp windows include additional sequence differences for some pairs (the paper reports 1,362 such pairs). Coordinates are supplied in both hg19 and hg38, with reference_genome set to hg19 because the primary oligo coordinates are hg19. Three biological replicates were performed for this cell type; per-replicate log2 fold-changes are retained from Supplementary file 1j. The GEO workbook aggregates replicates, so the eLife supplement is the primary source for the table. No treatment perturbation was reported.

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