Lentiviral MPRA in posterior neural progenitor cells (P-NPC)
Integrative analyses highlight functional regulatory variants associated with neuropsychiatric diseasesThe candidate variant library was assayed in in-vitro differentiated posterior neural progenitor cells. The posterior neural program used SB431542, LDN193189 and CHIR99021 before barcode RNA/plasmid DNA quantification.
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
Posterior neural differentiation with SB431542 + LDN193189 + CHIR99021
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: P-NPC_1=GSM6862277; P-NPC_2=GSM6862278; P-NPC_3=GSM6862279; P-NPC_4=GSM6862280. The paper's nomenclature calls the genome assembly hg19/hg37; this package represents it as GRCh37. The S5 P-NPC worksheet has no variant-name column (only sequential row numbers). Published condition-specific statistic/p/FDR/log2FC fields are therefore left blank rather than guessed; the 333 retained P-NPC daSNV coordinates come from Data3's mpra_tissue annotation and are paired with GEO count-derived fields. 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.