Cue-specific condition of the cross-disorder allele-specific lentiMPRA library in mature human iGLUTs exposed to recombinant IL-6. The shared integrated lentiMPRA library of 9,244 allele-specific candidate regulatory sequences and 100 scramble controls was measured in mature hiPSC-derived glutamatergic neurons from two neurotypical donors.
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.
Organism
Human
Taxonomy ID
NCBITaxon:9606
Biosample
CL:0000679
Reference genome
GRCh38
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
60 ng/mL recombinant human IL-6 for 48h
An integrated lentiMPRA library tested 9,244 allele-specific candidate regulatory sequences representing 4,622 biallelic SNPs plus 100 scramble controls. The 199/200-bp inserts were cloned with a minimal promoter and random 15-bp barcode into the pLS-SceI lentiviral reporter vector, packaged, and spinfected into mature day-21 iGLUTs. Two neurotypical donor hiPSC lines (#3182, XX; #2607, XY) were tested with two biological replicates per condition; cells were harvested 72 hours after infection following 48 hours of cue exposure, and reporter DNA/RNA was sequenced on an Illumina NextSeq 2x50. The processed table preserves the authors’ quantification and allele-effect statistics and adds cue-by-variant interaction statistics from SI Data 2.15 and 2.16 when a variant-level match was available.
Processed data
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Visible columns (39 of 39)
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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 · 39 definitions
element_id
Exact candidate regulatory sequence identifier (CRS) from the authors’ condition-specific MPRA summary table; allele is included in the identifier.
variant_id
dbSNP rs identifier; blank for scramble controls or records without a resolvable rsID.
chromosome
GRCh38 chromosome parsed from the authors’ ID field, without the chr prefix.
position_grch38
1-based GRCh38 position parsed from the authors’ ID field.
allele_type
Reference (ref) or alternative (alt) allele label supplied by the authors; blank for scramble controls.
allele
Nucleotide sequence allele supplied by the authors; blank for scramble controls.
sequence
The 199/200-bp MPRA insert sequence from Supplementary Data 2.9.
sequence_length_bp
Length of the supplied MPRA insert sequence in base pairs.
prioritization_methods
Unique library-prioritization labels from the source row(s), joined with semicolons when multiple labels apply.
e_genes
Unique eGene Ensembl identifiers associated with the candidate, joined with semicolons.
gwas_traits
Unique GWAS trait/disorder labels associated with the candidate, joined with semicolons.
source_datasets
Unique source-study labels associated with the candidate, joined with semicolons.
annotation_notes
Unique annotation notes from the source table, joined with semicolons.
activity_log2fc
Authors’ quantification log2 fold-change for reporter output activity relative to DNA input.
activity_average_expression
Authors’ average expression statistic for the activity model.
activity_t
Authors’ t-statistic for the activity model.
activity_pvalue
Authors’ nominal p-value for activity relative to DNA input.
Authors’ MPRA candidate regulatory sequence class (activated, repressed, or not significant at the listed FDR threshold).
variant_effect_log2fc
Authors’ allele-specific variant-effect log2 fold-change (emVar) comparing alternative and reference alleles.
variant_effect_average_expression
Authors’ average expression statistic for the variant-effect model.
variant_effect_t
Authors’ t-statistic for the variant-effect model.
variant_effect_pvalue
Authors’ nominal p-value for the variant-effect model.
variant_effect_fdr
Authors’ multiple-testing-adjusted p-value for the variant-effect model.
variant_effect_bayes_factor
Authors’ B statistic for the variant-effect model.
variant_effect_qvalue
Authors’ Storey q-value for the variant effect.
variant_effect_class
Authors’ variant-effect significance class (FDR <= 0.05, FDR <= 0.1, or not significant); blank when not tested for a scramble.
il6_vs_baseline_interaction_log2fc
Authors’ IL-6 versus baseline cue-by-variant interaction log2 fold-change, joined by variant ID from SI Data 2.15.
il6_vs_baseline_interaction_pvalue
Authors’ nominal p-value for the IL-6 versus baseline cue-by-variant interaction.
il6_vs_baseline_interaction_fdr
Authors’ FDR-adjusted p-value for the IL-6 versus baseline cue-by-variant interaction.
il6_vs_baseline_interaction_qvalue
Authors’ Storey q-value for the IL-6 versus baseline cue-by-variant interaction.
ifna_vs_baseline_interaction_log2fc
Authors’ IFNα versus baseline cue-by-variant interaction log2 fold-change, joined by variant ID from SI Data 2.16.
ifna_vs_baseline_interaction_pvalue
Authors’ nominal p-value for the IFNα versus baseline cue-by-variant interaction.
ifna_vs_baseline_interaction_fdr
Authors’ FDR-adjusted p-value for the IFNα versus baseline cue-by-variant interaction.
ifna_vs_baseline_interaction_qvalue
Authors’ Storey q-value for the IFNα versus baseline cue-by-variant interaction.
condition
MPRA exposure condition represented by this experiment table.
qc_pass
TRUE for every retained row because the source condition table is the authors’ post-QC filtered summary; no failed source rows were included.
Quality control
The authors’ MPRAflow count workflow required at least 10 unique barcodes per insert and used 14-bp barcode/16-bp UMI counting with a count threshold of 10. They removed candidate regulatory sequences that failed technical-replicate reproducibility, using outlier testing on replicate RNA/DNA activity differences (outside Q1 - 1.5xIQR or Q3 + 1.5xIQR), and reported strong replicate correlations after filtering. The supplied condition-specific tables are already the authors’ filtered summaries, so this package retained their rows, collapsed only exact duplicate CRS annotations while preserving all unique annotations, joined the supplied sequences, and added qc_pass=TRUE; no additional raw-count filter was possible because barcode-level counts were not released.
Curation notes
The table is a condition-level, allele/CRS summary rather than raw barcode counts. It includes both active and inactive filtered elements, including scramble controls, because those controls provide the published minimal-promoter baseline. Multiple exact-CRS source rows were collapsed into one row with unique annotations joined by semicolons; quantitative results were identical across those duplicate annotation rows. Interaction results are variant-level joins and therefore repeat across the two alleles of a tested variant when available. The complete article body available at ingestion was the open-access PMC/bioRxiv manuscript; the final Nature Communications abstract and supplementary workbooks are preserved and identified in the parent metadata.