Allelic variant lentiMPRA in human cortical organoid slices
Massively parallel characterization of regulatory elements in the developing human cortexThe 270-bp brain QTL and psychiatric-disorder-associated variant library was tested with reference and alternative alleles in approximately 10-week human cortical organoid slices. The table retains allele-specific RNA/DNA activity, limma statistics, and the supplied regulatory annotations.
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; approximately 10-week human cortical organoid slices
The variant library used 270-bp inserts centered on each variant, a 31-bp minimal promoter, and a 15-bp random barcode in a lentiviral reporter integrated into organoid cells. Reference and alternative allele activities are CPM-normalized RNA/DNA ratios; the source supplies the alternative/reference ratio and limma allelic-effect statistics for the organoid condition.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (35 of 35)
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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 · 35 definitions
- variant_id
- Variant rsID from the source library.
- variant_chromosome
- Chromosome of the variant in GRCh38.
- variant_position
- GRCh38 position of the variant.
- insert_id
- Source identifier for the 270-bp reporter insert containing the variant.
- insert_start
- Source start coordinate of the reporter insert.
- insert_end
- Source end coordinate of the reporter insert.
- insert_length_bp
- Derived insert length in base pairs, calculated as insert_end minus insert_start.
- alt_ref_ratio
- Source alternative-allele activity divided by reference-allele activity.
- log2_alt_ref_ratio
- Derived base-2 logarithm of alt_ref_ratio.
- alt_activity_rna_dna_ratio
- Source CPM-normalized RNA/DNA activity for the alternative allele.
- ref_activity_rna_dna_ratio
- Source CPM-normalized RNA/DNA activity for the reference allele.
- alt_is_active
- Source active/inactive call for the alternative allele.
- ref_is_active
- Source active/inactive call for the reference allele.
- limma_logFC
- Source limma log2 fold-change for the alternative allele relative to the reference allele.
- limma_p_value
- Source limma nominal P value for the allelic activity test.
- limma_adjusted_p_value
- Source multiple-testing-adjusted limma P value.
- effect_direction
- Derived direction of the limma effect: increased, decreased, or no_effect.
- reported_da_1pct
- Derived 1% FDR differential-activity flag: adjusted P <0.01 and absolute limma logFC >0.5.
- reported_da_10pct
- Derived 10% FDR differential-activity flag: adjusted P <0.10 and absolute limma logFC >0.5.
- atac_cell_types
- Semicolon-separated cell types whose ATAC-seq annotations overlap the variant insert.
- da_cell_types
- Semicolon-separated cell types whose differentially accessible annotations overlap the variant insert.
- qtl_sources
- Semicolon-separated QTL datasets in which the variant or linked variant is annotated.
- gwas_ld_traits
- Semicolon-separated psychiatric or neurological GWAS traits linked by LD in the source annotations.
- closest_cross_disorder_gene
- Closest cross-disorder differentially expressed gene name from the source annotation.
- closest_cross_disorder_distance_bp
- Distance in base pairs to the closest cross-disorder differentially expressed gene.
- qtl_target_id
- Source identifier of a predicted QTL target gene.
- qtl_target_name
- Source name of a predicted QTL target gene.
- qtl_target_tpm_mean
- Source mean TPM expression for the predicted QTL target gene.
- loop_target_genes
- Unique promoter target genes aggregated from source chromatin-loop annotations.
- abc_target_genes
- Unique target gene names from Activity-by-Contact annotations.
- motifbreakr_gene
- Transcription-factor gene whose motif is predicted to be altered by the allele, from motifbreakR.
- motifbreakr_effect_size
- Source motifbreakR effect-size annotation.
- motifbreakr_effect
- Source motifbreakR qualitative effect annotation.
- qtl_conservation
- Source conservation score for the variant/QTL annotation.
- insert_conservation_mean
- Source mean evolutionary conservation score for the full reporter insert.
Quality control
The supplemental methods required merged reads with a 270M CIGAR, base quality >=30, barcode Shannon entropy >0.5, barcode observation >=3 times with >=90% assignment to the same insert, >=10 unique barcodes per insert, and >=40 total DNA barcodes. DNA/RNA counts were CPM-normalized; variant activity was computed from alternative and reference RNA/DNA ratios, and allelic effects were tested with limma including batch terms. Data S2 contains 15,495 organoid variant rows; 14,431 rows with finite alternative/reference activity and limma statistics were retained, while 1,064 rows missing one or more required numeric values were excluded. The processed reported_da flags use adjusted P <0.01 or <0.10 and absolute limma logFC >0.5.
Curation notes
This is the matched organoid allelic experiment and contains the QC-passed variant reporter results, not the upstream GWAS/QTL candidate list. The biosample is represented at the cerebral-cortex tissue level because the organoid is a mixed cortical model. Source rows lacking finite allele activities or limma statistics were excluded. The reported_da flags apply the same reproducible logFC/FDR rule as the primary experiment; they are derived for the supplied organoid statistics.