HMC3 microglia-like cell MPRA — IFN-β stimulation
Context-dependent regulatory variants in Alzheimer’s diseaseVariant-focused plasmid MPRA in HMC3 microglia-like cells stimulated with IFN-β. The same paired alternative/reference regulatory-variant library was quantified through reporter RNA/DNA ratios.
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
20 ng/mL IFN-β for 24 h
Synthetic 227-bp candidate CREs were cloned downstream of a minimal promoter in a barcoded plasmid reporter and transfected into HMC3 cells; enhancer RNA/DNA ratios were modeled with MPRAnalyze.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (54 of 54)
| Row | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 11 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 12 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 13 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 14 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 15 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 20 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 29 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 30 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 31 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 32 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 33 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 34 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 35 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 36 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 37 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 38 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 39 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 40 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 41 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 42 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 43 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 44 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 45 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 46 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 47 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 48 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 49 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 50 |
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 54 definitions
- construct_id
- Alternative-allele MPRA construct identifier from the study design.
- reference_construct_id
- Reference/background construct paired to construct_id in the study’s MPRA_REF_ALT mapping.
- variant_id
- Variant identifier (usually dbSNP rsID; includes cg IDs for methylation-array-derived candidates).
- chromosome
- GRCh38 chromosome number for the tested construct.
- position_hg38
- GRCh38 position of the indexed candidate variant, taken from the study’s construct-aligned snp(hg19+hg38) field; raw source fields are preserved in media-3.xlsx.
- reference_allele
- Reference allele recorded in the study design.
- alternate_allele
- Alternate allele represented by construct_id.
- major_allele
- Allele designated Major by the study’s population annotation.
- minor_allele
- Allele designated Minor by the study’s population annotation.
- refalt_flip
- Study flag indicating whether the reported reference/alternate orientation is flipped relative to Major/Minor.
- construct_center_type
- Whether the construct was centered on a SNP or a regulatory peak.
- peak_start_hg38
- Start of the broad GRCh38 MPRA construct interval.
- peak_end_hg38
- End of the broad GRCh38 MPRA construct interval.
- peak_summit_hg38
- GRCh38 center/summit used for the construct.
- closest_protein_coding_gene
- Closest protein-coding gene to the tested locus according to the study annotation.
- distance_to_closest_protein_coding_tss
- Distance in base pairs to the closest protein-coding transcription start site.
- regulatory_annotation
- Hierarchical regulatory annotation from the study.
- rsid_gene_tss_annotation
- Study’s variant-to-gene/TSS annotation label.
- cre_annotation
- Candidate cis-regulatory-element annotation.
- rare_common
- Study classification of the candidate as Rare or Common.
- gc_content
- GC content value reported for the tested sequence (the supplement expresses this as a percentage-like value).
- gwas_bellenguez_p_value
- Bellenguez et al. GWAS p-value recorded by the study.
- gwas_bellenguez_neg_log10_p
- Negative log10 of the Bellenguez et al. GWAS p-value.
- motif_mef2
- Study motif annotation for MEF2.
- motif_pu1
- Study motif annotation for PU.1.
- motif_irf
- Study motif annotation for IRF.
- motif_stat
- Study motif annotation for STAT.
- motif_nf_kappa_b
- Study motif annotation for NF-κB.
- motif_ap1
- Study motif annotation for AP-1.
- allelic_log2fc_major_vs_minor
- MPRAnalyze allelic effect normalized to Major minus Minor log2 reporter activity.
- allelic_statistic
- MPRAnalyze test statistic for the allelic comparison.
- allelic_p_value
- Unadjusted MPRAnalyze p-value for the allelic comparison.
- allelic_fdr
- FDR-adjusted MPRAnalyze p-value for the allelic comparison.
- allelic_df_test
- Degrees of freedom for the allelic test.
- allelic_df_dna
- DNA-model degrees of freedom for the allelic test.
- allelic_df_rna_full
- Full RNA-model degrees of freedom for the allelic test.
- allelic_df_rna_reduced
- Reduced RNA-model degrees of freedom for the allelic test.
- major_activity_mad_score
- MPRAnalyze MAD activity score for the Major-allele construct.
- minor_activity_mad_score
- MPRAnalyze MAD activity score for the Minor-allele construct.
- major_activity_p_mad
- MPRAnalyze MAD activity p-value for the Major-allele construct.
- minor_activity_p_mad
- MPRAnalyze MAD activity p-value for the Minor-allele construct.
- major_activity_z_score
- MPRAnalyze z-score for the Major-allele construct.
- minor_activity_z_score
- MPRAnalyze z-score for the Minor-allele construct.
- major_activity_p_zscore
- MPRAnalyze z-score p-value for the Major-allele construct.
- minor_activity_p_zscore
- MPRAnalyze z-score p-value for the Minor-allele construct.
- enhancer_activity_qc
- TRUE when either allele has study-defined active-enhancer pval.mad < 0.05; FALSE otherwise.
- emvar_qc
- TRUE when the study-defined allelic FDR is < 0.05; FALSE otherwise.
- stimulus_vs_resting_log2fc
- Construct-level activity log2 fold-change versus the matched resting state, when reported.
- stimulus_vs_resting_p_value
- Unadjusted p-value for construct activity change versus the matched resting state, when reported.
- stimulus_vs_resting_fdr
- FDR for construct activity change versus the matched resting state, when reported.
- ml_predicted_log2fc_model_1
- Study-reported interpretable ML predicted chromatin log2 fold-change for model 1; blank where no exact context model was supplied.
- ml_predicted_log2fc_model_2
- Study-reported interpretable ML predicted chromatin log2 fold-change for model 2; blank where no exact context model was supplied.
- ml_prediction_model_1
- Name of the ML prediction column used for model 1.
- ml_prediction_model_2
- Name of the ML prediction column used for model 2.
Quality control
The study excluded 21 enhancers with underrepresented genomic-DNA barcode counts and used 15 barcode replicates for the standard analyses; its sparse brain and THP-1 monocyte datasets were handled with five pseudo-barcodes formed by summing groups of three. For this package, only non-empty alternative constructs with an exact design record, an explicit alt-to-reference mapping, matching activity rows for both paired constructs, and numeric MPRAnalyze allelic statistics were retained. The enhancer_activity_qc and emvar_qc columns expose the study thresholds (pval.mad < 0.05 and FDR < 0.05) without removing biologically inactive or non-significant tested variants.
Curation notes
For some constructs, the supplement’s pos_hg38/coordinate fields disagree with the construct-aligned snp(hg19+hg38) value and encoded construct interval; position_hg38 in this processed table follows the latter so it matches the assayed sequence, while the raw workbook preserves the original fields. The table also carries construct-level activity change versus HMC3_Naive from Supplementary Table 5. No exact HMC3 column is present in the manuscript’s ML prediction table, so those fields are blank.