Experiment / E98JJGR1ZAAV-MPRA / in vivo MPRA

AAV9 in vivo 5′UTR MPRA in CreON glutamatergic cortical neurons

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

Approximately 500 allelic reporter pairs per AAV sublibrary were delivered to neonatal mouse cortex and assayed at postnatal day 21. Cre-dependent primer inversion selectively captured reporter RNA from Vglut-positive glutamatergic neurons, and input, DNA, monosome/80S, and polysome fractions were used to quantify allele-dependent translation effects.

Download processed table (CSV)Raw source data API documentation

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: Mouse
Taxonomy ID: NCBITaxon:10090
Biosample: CL:0000679
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; CreON / Vglut-positive glutamatergic neuron readout

AAV9-packaged episomal reporter library with Cre-dependent inversion of the RT primer cassette; three approximately 500-allelic-pair sublibraries (JD487–JD489) and six biological animals per sublibrary. CreON results include input/DNA, monosome/input, polysome/input, and polysome/monosome comparisons. The study excluded CreOFF 80S/monosome measurements because of low barcode recovery and replicate correlation.

Processed data

50 rows per page. Click a cell to inspect its full value.

Search table valuesFilter columnOperatorValue

Visible columns (65 of 65)

Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50

Page 1 · 50 rows · More results available

Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.

Column dictionary · 65 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.
monosome_vs_input_log2FC: Author-reported oriented log2 fold change for monosome_vs_input; positive values favor the numerator named in the label.
monosome_vs_input_pvalue: Model-based allele-effect p-value for monosome_vs_input.
monosome_vs_input_LRT_pvalue: Likelihood-ratio test p-value for the allele effect in monosome_vs_input.
monosome_vs_input_tstat: Allele-term test statistic for monosome_vs_input.
monosome_vs_input_fdr: Author-reported FDR value for monosome_vs_input.
monosome_vs_input_empirical_pvalue: Empirical allele-effect p-value from the author’s 10,000 blank-control null comparisons for monosome_vs_input.
monosome_vs_input_qvalue: Author-reported q-value (multiple-testing corrected empirical p-value) for monosome_vs_input.
polysome_vs_monosome_log2FC: Author-reported oriented log2 fold change for polysome_vs_monosome; positive values favor the numerator named in the label.
polysome_vs_monosome_pvalue: Model-based allele-effect p-value for polysome_vs_monosome.
polysome_vs_monosome_LRT_pvalue: Likelihood-ratio test p-value for the allele effect in polysome_vs_monosome.
polysome_vs_monosome_tstat: Allele-term test statistic for polysome_vs_monosome.
polysome_vs_monosome_fdr: Author-reported FDR value for polysome_vs_monosome.
polysome_vs_monosome_empirical_pvalue: Empirical allele-effect p-value from the author’s 10,000 blank-control null comparisons for polysome_vs_monosome.
polysome_vs_monosome_qvalue: Author-reported q-value (multiple-testing corrected empirical p-value) for polysome_vs_monosome.
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 the same 20-UMI-per-fraction barcode filter, required at least three biological replicates with at least three reference and three alternative barcodes, fit barcode-level mixed effects models, and used 10,000 blank-control null comparisons with q-value correction. For this package, rows with at least one complete author-reported CreON comparison are retained; incomplete comparison-specific results remain blank. The source analysis was performed separately for each AAV sublibrary.

Curation notes

This table contains 1463 QC-retained variant/transcript contexts across the three sublibraries. Source files use CreN for the CreON state. The paper’s methods name a Vglut1-IRES2-Cre-D mouse line while the results and GEO sample labels describe Vglut-positive/Vglut2-positive glutamatergic neurons; the biosample is therefore represented at the resolved terminal cell-type level rather than asserting a strain-specific ontology term. LogFC signs for MvP were reversed to report polysome-versus-monosome effects as in the author’s supplemental-table code.

Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50

Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50

Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50