Experiment / E13PWBUSYAAV-MPRA / in vivo MPRA

AAV9 in vivo 5′ UTR MPRA in Vglut2-positive glutamatergic neurons

Approaches for identification of 5′ UTR mutations impacting translation and protein production from neurodevelopmental disorder genes

Three AAV9 sublibraries, each containing approximately 500 reference/alternate 5′ UTR allele pairs, were delivered transcranially to neonatal mouse cortex and assayed at postnatal day 21. A Cre-dependent reverse-transcription switch separated Vglut2-positive glutamatergic-neuron (CreON) measurements from non-Cre-expressing transduced cells (CreOFF), with DNA, input RNA, monosome, and polysome readouts across six animals per sublibrary.

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Organism: Mouse
Taxonomy ID: NCBITaxon:10090
Biosample: CL:0000679
Reference genome: GRCh38
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

AAV9 transcranial delivery at P1; cortical collection at P21; CreON/CreOFF cell-type readout

AAV9-packaged episomal reporter library with Cre-dependent inversion of the RT-primer cassette. Sublibraries JD487, JD488, and JD489 were analyzed with six animals each; the table includes CreON and CreOFF allelic effects plus allele×Cre interaction results. The authors excluded CreOFF 80S/monosome measurements because of low barcode recovery and replicate correlation.

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Column dictionary · 121 definitions

reporter_context_id: Normalized identifier for a unique variant/transcript sequence context in the MPRA library.
variant_id: Chromosome and coordinate portion of the tested variant identifier.
chromosome: Human chromosome for the reporter’s tested variant.
start: Annotated 1-based variant start coordinate.
end: Annotated 1-based variant end coordinate.
strand: Annotated transcript strand.
reference_allele: Reference allele used in the reference reporter.
alternate_allele: Alternate allele used in the mutant reporter.
family_id: Neurodevelopmental-disorder family identifier from the source library.
sample_id: Source sample/context identifier.
gene_id: Ensembl gene identifier.
gene_symbol: Gene symbol.
phenotype: Source variant class, case or control.
transcript_accession: Transcript accession used for sequence annotation.
transcript_id: Ensembl transcript identifier represented by the reporter.
duplicate_ids: Source duplicate-context identifiers, when present.
reference_sequence: Reference 5′ UTR reporter sequence inserted into the construct.
alternate_sequence: Alternate 5′ UTR reporter sequence inserted into the construct.
reference_sequence_length: Length in nucleotides of the reference reporter sequence.
alternate_sequence_length: Length in nucleotides of the alternate reporter sequence.
relative_variant_start: Variant start relative to the sequence context.
relative_variant_end: Variant end relative to the sequence context.
relative_coding_start: Coding-start position relative to the sequence context.
final_atg_position: Position of the final canonical ATG in the designed reporter context.
final_rf_shift: Source reading-frame adjustment for the designed context.
reference_mfe: Predicted minimum free energy of the reference sequence.
alternate_mfe: Predicted minimum free energy of the alternate sequence.
delta_mfe: Source alternate-minus-reference MFE difference.
reference_uorf_count: Predicted/annotated upstream open-reading-frame count in the reference sequence.
alternate_uorf_count: Predicted/annotated upstream open-reading-frame count in the alternate sequence.
uorf_change: Source indicator of an upstream ORF gain/loss or change.
uaug_context_perturbed: Indicator that the variant perturbs an upstream AUG context.
any_gtex_brain_expressed: Indicator that any represented transcript is expressed in GTEx brain data.
pli: Probability of loss-of-function intolerance annotation.
sfari_gene_score: SFARI gene evidence score.
sfari_gene_syndromic: SFARI syndromic-gene indicator.
sfari_gene_denovo: SFARI de novo-gene indicator.
assigned_sublibrary: AAV variant sublibrary assigned from the dominant CreON DNA signal: 487, 488, or 489.
designed_barcodes_reference: Number of reference-allele barcode rows in the source count matrix/library design.
designed_barcodes_alternate: Number of alternate-allele barcode rows in the source count matrix/library design.
observed_barcodes_reference: Number of reference barcode rows retained in the assigned-sublibrary GEO matrix.
observed_barcodes_alternate: Number of alternate barcode rows retained in the assigned-sublibrary GEO matrix.
significant_metric_count_q05: Number of listed allelic effect comparisons with author q-value below 0.05.
qc_pass: Package QC flag; true for contexts retained from the author’s complete CreON core result set.
audit_umi_threshold: UMI threshold used for the independent raw-count barcode audit, 20 counts per fraction.
audit_creon_replicates_input_dna: Number of CreON animals with at least three reference and three alternate barcodes passing the 20-UMI threshold for input RNA/DNA.
audit_creon_ref_barcodes_min_input_dna: Minimum passing CreON reference barcode count across qualifying input RNA/DNA animals.
audit_creon_alt_barcodes_min_input_dna: Minimum passing CreON alternate barcode count across qualifying input RNA/DNA animals.
audit_creon_replicates_monosome_input: Number of qualifying CreON animals for the monosome/input count audit.
audit_creon_ref_barcodes_min_monosome_input: Minimum passing CreON reference barcode count for the monosome/input audit.
audit_creon_alt_barcodes_min_monosome_input: Minimum passing CreON alternate barcode count for the monosome/input audit.
audit_creon_replicates_polysome_monosome: Number of qualifying CreON animals for the polysome/monosome count audit.
audit_creon_ref_barcodes_min_polysome_monosome: Minimum passing CreON reference barcode count for the polysome/monosome audit.
audit_creon_alt_barcodes_min_polysome_monosome: Minimum passing CreON alternate barcode count for the polysome/monosome audit.
audit_creon_replicates_polysome_input: Number of qualifying CreON animals for the polysome/input count audit.
audit_creon_ref_barcodes_min_polysome_input: Minimum passing CreON reference barcode count for the polysome/input audit.
audit_creon_alt_barcodes_min_polysome_input: Minimum passing CreON alternate barcode count for the polysome/input audit.
mean_umi_creon_ref_dna: Mean unnormalized CreON DNA UMI count for reference barcode rows in the assigned sublibrary.
mean_umi_creon_alt_dna: Mean unnormalized CreON DNA UMI count for alternate barcode rows in the assigned sublibrary.
mean_umi_creon_ref_input: Mean unnormalized CreON input-RNA UMI count for reference barcode rows.
mean_umi_creon_alt_input: Mean unnormalized CreON input-RNA UMI count for alternate barcode rows.
mean_umi_creon_ref_monosome: Mean unnormalized CreON monosome UMI count for reference barcode rows.
mean_umi_creon_alt_monosome: Mean unnormalized CreON monosome UMI count for alternate barcode rows.
mean_umi_creon_ref_polysome: Mean unnormalized CreON polysome UMI count for reference barcode rows.
mean_umi_creon_alt_polysome: Mean unnormalized CreON polysome UMI count for alternate barcode rows.
mean_umi_creoff_ref_dna: Mean unnormalized CreOFF DNA UMI count for reference barcode rows.
mean_umi_creoff_alt_dna: Mean unnormalized CreOFF DNA UMI count for alternate barcode rows.
mean_umi_creoff_ref_input: Mean unnormalized CreOFF input-RNA UMI count for reference barcode rows.
mean_umi_creoff_alt_input: Mean unnormalized CreOFF input-RNA UMI count for alternate barcode rows.
mean_umi_creoff_ref_monosome: Mean unnormalized CreOFF monosome UMI count for reference barcode rows; this readout was not used for source CreOFF effect testing.
mean_umi_creoff_alt_monosome: Mean unnormalized CreOFF monosome UMI count for alternate barcode rows; this readout was not used for source CreOFF effect testing.
mean_umi_creoff_ref_polysome: Mean unnormalized CreOFF polysome UMI count for reference barcode rows.
mean_umi_creoff_alt_polysome: Mean unnormalized CreOFF polysome UMI count for alternate barcode rows.
creon_total_rna_dna_logfc: Author-reported CreON allelic log2 fold change for Table S5.1 CreON Total RNA-DNA.
creon_total_rna_dna_empirical_pvalue: Author empirical p-value for Table S5.1.
creon_total_rna_dna_qvalue: Author multiple-testing-corrected q-value for Table S5.1.
creon_total_rna_dna_significant_q05: Derived true when creon_total_rna_dna_qvalue is below 0.05.
creon_monosome_total_rna_logfc: Author-reported CreON allelic log2 fold change for Table S5.2 CreON Monosome-Total RNA.
creon_monosome_total_rna_empirical_pvalue: Author empirical p-value for Table S5.2.
creon_monosome_total_rna_qvalue: Author multiple-testing-corrected q-value for Table S5.2.
creon_monosome_total_rna_significant_q05: Derived true when creon_monosome_total_rna_qvalue is below 0.05.
creon_monosome_polysome_logfc: Author-reported CreON allelic log2 fold change for Table S5.3 CreOn Monosome-Polysome; source orientation is preserved.
creon_monosome_polysome_empirical_pvalue: Author empirical p-value for Table S5.3.
creon_monosome_polysome_qvalue: Author multiple-testing-corrected q-value for Table S5.3.
creon_monosome_polysome_significant_q05: Derived true when creon_monosome_polysome_qvalue is below 0.05.
creon_polysome_total_rna_logfc: Author-reported CreON allelic log2 fold change for Table S5.4 CreON Polysome-Total RNA.
creon_polysome_total_rna_empirical_pvalue: Author empirical p-value for Table S5.4.
creon_polysome_total_rna_qvalue: Author multiple-testing-corrected q-value for Table S5.4.
creon_polysome_total_rna_significant_q05: Derived true when creon_polysome_total_rna_qvalue is below 0.05.
creoff_total_rna_dna_logfc: Author-reported CreOFF allelic log2 fold change for Table S5.5 CreOFF Total RNA-DNA.
creoff_total_rna_dna_empirical_pvalue: Author empirical p-value for Table S5.5.
creoff_total_rna_dna_qvalue: Author multiple-testing-corrected q-value for Table S5.5.
creoff_total_rna_dna_significant_q05: Derived true when creoff_total_rna_dna_qvalue is below 0.05.
creoff_polysome_total_rna_logfc: Author-reported CreOFF allelic log2 fold change for Table S5.6 CreOFF Polysome-Total RNA.
creoff_polysome_total_rna_empirical_pvalue: Author empirical p-value for Table S5.6.
creoff_polysome_total_rna_qvalue: Author multiple-testing-corrected q-value for Table S5.6.
creoff_polysome_total_rna_significant_q05: Derived true when creoff_polysome_total_rna_qvalue is below 0.05.
interaction_total_rna_dna_allele_lfc: Source Table S5.7 Allele_LFC for the total RNA-DNA allele×Cre interaction model.
interaction_total_rna_dna_cre_lfc: Source Table S5.7 Cre_LFC for the total RNA-DNA allele×Cre interaction model.
interaction_total_rna_dna_allele_x_cre_lfc: Source Table S5.7 allele×Cre interaction log fold change for total RNA-DNA.
interaction_total_rna_dna_allele_empirical_pvalue: Source Table S5.7 empirical p-value for the allele term.
interaction_total_rna_dna_allele_qvalue: Source Table S5.7 q-value for the allele term.
interaction_total_rna_dna_cre_empirical_pvalue: Source Table S5.7 empirical p-value for the Cre term.
interaction_total_rna_dna_cre_qvalue: Source Table S5.7 q-value for the Cre term.
interaction_total_rna_dna_allele_x_cre_empirical_pvalue: Source Table S5.7 empirical p-value for the allele×Cre term.
interaction_total_rna_dna_allele_x_cre_qvalue: Source Table S5.7 q-value for the allele×Cre term.
interaction_total_rna_dna_allele_significant_q05: Derived true when the Table S5.7 allele-term q-value is below 0.05.
interaction_total_rna_dna_cre_significant_q05: Derived true when the Table S5.7 Cre-term q-value is below 0.05.
interaction_total_rna_dna_allele_x_cre_significant_q05: Derived true when the Table S5.7 allele×Cre q-value is below 0.05.
interaction_polysome_total_rna_allele_lfc: Source Table S5.8 Allele_LFC for the polysome-total RNA allele×Cre interaction model.
interaction_polysome_total_rna_cre_lfc: Source Table S5.8 Cre_LFC for the polysome-total RNA allele×Cre interaction model.
interaction_polysome_total_rna_allele_x_cre_lfc: Source Table S5.8 allele×Cre interaction log fold change for polysome-total RNA.
interaction_polysome_total_rna_allele_empirical_pvalue: Source Table S5.8 empirical p-value for the allele term.
interaction_polysome_total_rna_allele_qvalue: Source Table S5.8 q-value for the allele term.
interaction_polysome_total_rna_cre_empirical_pvalue: Source Table S5.8 empirical p-value for the Cre term.
interaction_polysome_total_rna_cre_qvalue: Source Table S5.8 q-value for the Cre term.
interaction_polysome_total_rna_allele_x_cre_empirical_pvalue: Source Table S5.8 empirical p-value for the allele×Cre term.
interaction_polysome_total_rna_allele_x_cre_qvalue: Source Table S5.8 q-value for the allele×Cre term.
interaction_polysome_total_rna_allele_significant_q05: Derived true when the Table S5.8 allele-term q-value is below 0.05.
interaction_polysome_total_rna_cre_significant_q05: Derived true when the Table S5.8 Cre-term q-value is below 0.05.
interaction_polysome_total_rna_allele_x_cre_significant_q05: Derived true when the Table S5.8 allele×Cre q-value is below 0.05.

Quality control

The authors removed barcode observations with fewer than 20 UMI counts in either fraction of a ratiometric measurement, required at least three biological replicates with at least three reference and three alternate barcodes after filtering, and used blank-control empirical p-values with q-value correction. For cell-context and allele×Cre tests, CreON and CreOFF libraries also had to share qualifying replicates; CreOFF 80S/monosome measurements were excluded for low recovery. The package retains 1,273 contexts with complete author-reported q-values for all four CreON core allelic comparisons (Table S5.1–S5.4); incomplete comparison-specific CreOFF and interaction results remain blank.

Curation notes

This table is one row per tested variant/transcript context, combining the in vivo AAV MPRA source sheets with the library annotation and GEO UMI count audit. The genomic coordinates and UTR annotations are human GRCh38 reporter sequences assayed in mouse cortex. The retained set is defined by complete author-reported q-values in the four CreON core allelic sheets; comparison-specific CreOFF and interaction values may be blank. The audit columns are recomputed from the combined GEO matrix and are retained for transparency because that export does not exactly reproduce every source filtering decision. The in vivo workbook is publisher asset mmc6.xlsx and labels itself Supplemental Table 5, although the PMC associated-data text refers to the in vivo results as Table S4.

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