Experiment / E5LHJ5567AAV-MPRA / in vivo MPRA

AAV9 in vivo 5′UTR MPRA in CreOFF cortical cells

A Massively Parallel Screen of 5′UTR Mutations Identifies Variants Impacting Translation and Protein Production in Neurodevelopmental Disorder Genes

The same neonatal AAV9 reporter libraries were assayed with the non-inverted RT primer cassette to measure transduced, non-Cre-expressing cortical cells. DNA, input RNA, and polysome-associated RNA were used for allele-specific transcript-abundance and translation comparisons.

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Organism: Mouse
Taxonomy ID: NCBITaxon:10090
Biosample: UNMAPPED:non-Cre-expressing cells in mouse cortex
Reference genome: Not reported / not applicable
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

AAV9 transcranial delivery at P1; cortical collection at P21; CreOFF / non-Cre-expressing cortical-cell readout

CreOFF is the matched non-inverted RT-primer state from the in vivo AAV MPRA. The study reported input/DNA and polysome/input effects for CreOFF; 80S/monosome-derived CreOFF measurements were excluded because of low barcode recovery and replicate correlation.

Processed data

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Column dictionary · 51 definitions

reporter_context_id: Unique normalized variant/transcript reporter context identifier from the study library.
variant_id: Chromosome and genomic position identifying the tested variant.
transcript_id: Ensembl transcript identifier represented by the context.
gene_id: Ensembl gene identifier from the library annotation.
gene_symbol: HGNC gene symbol from the library annotation.
case_control: Original An et al. variant class: proband case or unaffected sibling control.
chromosome: Chromosome of the patient variant.
position: Variant genomic coordinate as reported in the library annotation.
ref_allele: Reference allele in the variant identifier.
alt_allele: Alternative allele in the variant identifier.
family_id: Family identifier from the source variant collection.
sample_id: Source sample/context identifier from the annotated library.
strand: Annotated transcript strand.
annotation_accession: Transcript accession used for library annotation.
ref_5utr_sequence: Reference synthetic 5′UTR reporter sequence used for this context.
alt_5utr_sequence: Alternative synthetic 5′UTR reporter sequence used for this context.
ref_sequence_length: Length in nucleotides of the reference reporter 5′UTR sequence.
alt_sequence_length: Length in nucleotides of the alternative reporter 5′UTR sequence.
ref_mfe: Predicted minimum free energy for the reference sequence.
alt_mfe: Predicted minimum free energy for the alternative sequence.
delta_mfe: Alternative minus reference minimum free energy as supplied by the annotation.
ref_uorf_count: Number of annotated/predicted upstream open reading frames in the reference sequence.
alt_uorf_count: Number of annotated/predicted upstream open reading frames in the alternative sequence.
uorf_change: Source annotation’s uORF deletion/change indicator.
uaug_context_perturbed: Whether the variant perturbs a uAUG start-codon context.
hek_expression: HEK expression annotation for the represented transcript.
any_hek_expressed: Any-isoform HEK expression annotation.
transcript_brain_expressed: Brain expression annotation for the represented transcript.
any_brain_expressed: Any-isoform brain expression annotation.
sfari_gene_score: SFARI gene score annotation.
sfari_gene_syndromic: SFARI syndromic-gene annotation.
sfari_gene_denovo: SFARI de novo-gene annotation.
barcodes_designed_ref: Number of designed barcodes for the reference allele/context in the oligo library.
barcodes_designed_alt: Number of designed barcodes for the alternative allele/context in the oligo library.
sublibrary: In vivo AAV sublibrary (JD487, JD488, or JD489); blank for the pooled HEK result.
n_measures_with_complete_stats: Number of listed ratiometric comparisons with both an author log2FC and q-value after the study’s QC.
qc_status: Rows retained because they have a complete author-tested result for at least one listed comparison; the author’s barcode/replicate filters were applied upstream.
input_vs_DNA_log2FC: Author-reported oriented log2 fold change for input_vs_DNA; positive values favor the numerator named in the label.
input_vs_DNA_pvalue: Model-based allele-effect p-value for input_vs_DNA.
input_vs_DNA_LRT_pvalue: Likelihood-ratio test p-value for the allele effect in input_vs_DNA.
input_vs_DNA_tstat: Allele-term test statistic for input_vs_DNA.
input_vs_DNA_fdr: Author-reported FDR value for input_vs_DNA.
input_vs_DNA_empirical_pvalue: Empirical allele-effect p-value from the author’s 10,000 blank-control null comparisons for input_vs_DNA.
input_vs_DNA_qvalue: Author-reported q-value (multiple-testing corrected empirical p-value) for input_vs_DNA.
polysome_vs_input_log2FC: Author-reported oriented log2 fold change for polysome_vs_input; positive values favor the numerator named in the label.
polysome_vs_input_pvalue: Model-based allele-effect p-value for polysome_vs_input.
polysome_vs_input_LRT_pvalue: Likelihood-ratio test p-value for the allele effect in polysome_vs_input.
polysome_vs_input_tstat: Allele-term test statistic for polysome_vs_input.
polysome_vs_input_fdr: Author-reported FDR value for polysome_vs_input.
polysome_vs_input_empirical_pvalue: Empirical allele-effect p-value from the author’s 10,000 blank-control null comparisons for polysome_vs_input.
polysome_vs_input_qvalue: Author-reported q-value (multiple-testing corrected empirical p-value) for polysome_vs_input.

Quality control

The study used a 20-UMI-per-fraction barcode threshold, required at least three biological replicates with at least three reference and three alternative barcodes, and used barcode-level mixed effects models with 10,000 blank-control null comparisons and q-value correction. This table retains contexts with at least one complete author-reported CreOFF comparison; incomplete comparison-specific results remain blank. CreOFF 80S/monosome measurements were not used, consistent with the paper’s QC exclusion.

Curation notes

This is a condition-specific view of the same in vivo AAV libraries, not a separate library synthesis. It contains 1219 QC-retained contexts. Source files use CreF for the CreOFF state. The mixed-cell biosample cannot be resolved to a single terminal cell type, so it is explicitly marked UNMAPPED.

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