Lentiviral MPRA in differentiated IMR-32 neuroblastoma cells
Integrative analyses highlight functional regulatory variants associated with neuropsychiatric diseasesThe candidate variant library was tested after chemical differentiation of IMR-32 neuroblastoma cells. Barcode RNA and plasmid DNA were quantified for the reference and alternate inserts.
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
1 mM dibutyryl-cAMP + 2.5 uM BrdU for 6 days
Lentiviral integrated MPRA using 145-bp hg19/GRCh37 reference/alternate inserts, a 10-bp filler/linker between restriction sites, 20-bp barcodes (10 barcodes per genomic instance), plasmid DNA baseline and barcode RNA readout analyzed with MPRAnalyze v1.4.0.
Processed data
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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 · 30 definitions
- variant_id
- Variant coordinate in hg19/GRCh37, formatted chromosome:1-based-position.
- rs_id
- Linked dbSNP identifier from Supplementary Data 3; blank where unavailable.
- reference_allele
- Reference allele for the tested reference/alternate sequence pair.
- alternate_allele
- Alternate allele for the tested reference/alternate sequence pair.
- lead_snp
- Index/lead SNP(s) linked to the tested variant in Supplementary Data 3.
- diseases
- Abbreviated neuropsychiatric disease association(s) linked to the variant.
- gene_annotation
- Gene annotation associated with the variant in Supplementary Data 3.
- eGenes
- Genes nominated by eQTL/eGene sources in Supplementary Data 3.
- nearest_gene
- Nearest or primary annotated gene from Supplementary Data 3.
- annotated_mpra_significant_conditions
- MPRA conditions listed as significant for this daSNV in Supplementary Data 3.
- atac_context
- ATAC-seq tissue/cell context annotations from Supplementary Data 3.
- hichip_context
- HiChIP tissue/cell context annotations from Supplementary Data 3.
- annotation_mpra_pval_mean_across_sig_conditions
- Mean MPRA p-value across significant conditions as reported in Supplementary Data 3; not condition-specific.
- annotation_mpra_log2_fc_mean_across_sig_conditions
- Mean MPRA log2 fold change across significant conditions as reported in Supplementary Data 3; not condition-specific.
- barcode_count_ref
- Number of reference-allele barcode rows in the GEO count matrix.
- barcode_count_alt
- Number of alternate-allele barcode rows in the GEO count matrix.
- plasmid_dna_count_ref
- Aggregate plasmid DNA count for reference-allele barcode rows in the GEO matrix.
- plasmid_dna_count_alt
- Aggregate plasmid DNA count for alternate-allele barcode rows in the GEO matrix.
- rna_count_ref
- Aggregate RNA count across the condition's GEO replicate columns for reference barcode rows.
- rna_count_alt
- Aggregate RNA count across the condition's GEO replicate columns for alternate barcode rows.
- rna_detected_replicates_ref
- Number of condition replicates with nonzero aggregate reference RNA count.
- rna_detected_replicates_alt
- Number of condition replicates with nonzero aggregate alternate RNA count.
- raw_mean_log2_activity_ref
- Mean pseudocount-smoothed log2 RNA/DNA activity from GEO counts for the reference allele; sample-depth normalized.
- raw_mean_log2_activity_alt
- Mean pseudocount-smoothed log2 RNA/DNA activity from GEO counts for the alternate allele; sample-depth normalized.
- raw_log2_fc_alt_vs_ref
- Mean raw count-derived alternate-minus-reference log2 activity across GEO replicates; independent of the published MPRAnalyze estimate.
- published_statistic
- MPRAnalyze likelihood-ratio statistic from Supplementary Data 5 for this condition.
- published_p_value
- MPRAnalyze p-value from Supplementary Data 5 for this condition.
- published_fdr
- FDR-adjusted MPRAnalyze p-value from Supplementary Data 5 for this condition.
- published_log2_fc_alt_vs_ref
- Published MPRAnalyze alternate/reference log2 fold change from Supplementary Data 5 for this condition.
- raw_qc_pass
- Package-level QC flag; all retained rows have both allele groups and finite count-derived metrics in GEO.
Quality control
The paper used barcode concordance across biological replicates, RNA/plasmid model diagnostics, replicate reproducibility and exclusion of poorly replicating or poor-quality cultures; MPRAnalyze v1.4.0 likelihood-ratio p-values were FDR-adjusted. Published daSNVs were required to have FDR < 0.05 and absolute log2 fold change > 0.05. Package-level QC additionally required both Ref and all_alt groups to be present in the GEO matrix and all count-derived metrics to be finite. No arbitrary depth cutoff was added because the released GEO aggregation does not reproduce the S5 MPRAnalyze summaries exactly.
Curation notes
GEO sample columns: IMR.diff_1=GSM6862296; IMR.diff_2=GSM6862297; IMR.diff_3=GSM6862298. The paper's nomenclature calls the genome assembly hg19/hg37; this package represents it as GRCh37. S5 IMR.diff provides 1812 finite coordinate-labelled model results, of which 191 meet the published daSNV threshold; 1804 remained after requiring both allele groups and finite GEO-derived metrics. Raw GEO scores are provided as independently calculated, sample-depth-normalized log2 RNA/DNA activities and should not be interpreted as replacements for the published MPRAnalyze estimates.