N2a cell line 3′UTR MPRA with Input and TRAP RNA
A Cre-dependent massively parallel reporter assay allows for cell-type specific assessment of the functional effects of non-coding elements in vivoA Cre-dependent plasmid 3′UTR MPRA library containing 120-bp reference, variant, GC-matched shuffled, and synthetic control elements was transfected into mouse Neuro-2a cells. Six biological replicates were profiled from whole-cell Input RNA and eGFP-RPL10a TRAP RNA, with plasmid DNA used for abundance normalization.
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
Cre recombinase and eGFP-RPL10a co-transfection; basal culture conditions
Cre-dependent DiO tdTomato reporter with six 9-bp barcodes per 120-bp 3′UTR element. Input RNA measures steady-state transcript abundance; TRAP RNA measures ribosome occupancy and TRAP/Input is used as a translation-efficiency proxy.
Processed data
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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 · 47 definitions
- element_id
- Identifier for the synthesized 120-bp element, shared across its allele or control constructs.
- allele
- Construct class: ref, alt, shuf, or dnvctl.
- element_class
- Normalized construct class: genomic_reference, variant_alternate, GC_matched_shuffle, or synthetic_control.
- element_sequence
- Sequence tested in the reporter 3′UTR.
- sequence_length_bp
- Length of the tested element in base pairs.
- barcode_count_designed
- Number of designed 9-bp barcodes assigned to the construct; the library design used six.
- phenotype
- Phenotype or cohort label from the supplementary element annotation.
- source_variant
- Source variant or patient/cohort identifier from the supplementary annotation.
- family_id
- Family identifier from the supplementary annotation when available.
- sample_id
- Source sample identifier from the supplementary annotation when available.
- mouse_ortholog
- Mouse ortholog annotation for the source human element when available.
- gene
- Associated gene symbol from the supplementary annotation.
- transcript_id
- Associated transcript identifier from the supplementary annotation.
- ensembl_gene_id
- Associated Ensembl gene identifier from the supplementary annotation.
- hg38_position_tag
- Original hg38-style position tag from the supplementary annotation.
- chromosome
- Chromosome annotation for the source element.
- hg19_start
- Start coordinate on hg19 when available.
- strand
- Strand of the source element.
- reference_allele
- Reference allele reported for the source variant.
- alternate_allele
- Alternate allele reported for the source variant.
- oe_lof_upper
- gnomAD observed/expected loss-of-function upper-bound annotation when available.
- sc_ne_expression_higher_than_median
- Single-cell neocortical expression-above-median annotation.
- ctx_striatum_higher_than_median
- Cortical/striatal expression-above-median annotation.
- modeled_allele_count
- Number of allele or control classes represented by published activity summaries for this element.
- qc_pass
- True for rows retained after the published QC and availability of a numeric published activity.
- activity_log2_rna_dna
- Published Input-RNA activity, log2(normalized RNA / normalized plasmid DNA).
- activity_sem_log2_rna_dna
- Standard error of the published Input-RNA/DNA activity.
- activity_log2_trap_dna
- Published TRAP-RNA activity, log2(normalized TRAP RNA / normalized plasmid DNA), a ribosome-occupancy measure.
- activity_sem_log2_trap_dna
- Standard error of the published TRAP-RNA/DNA activity.
- activity_log2_trap_input
- Published translation-efficiency proxy, log2(normalized TRAP RNA / normalized Input RNA).
- activity_sem_log2_trap_input
- Standard error of the published TRAP/Input activity.
- ref_alt_log2fc_rna_dna
- Alt minus Ref difference in published Input-RNA/DNA activity, in log2 units.
- ref_shuf_log2fc_rna_dna
- Shuf minus Ref difference in published Input-RNA/DNA activity, in log2 units.
- ref_alt_log2fc_trap_input
- Alt minus Ref difference in published TRAP/Input activity, in log2 units.
- ref_shuf_log2fc_trap_input
- Shuf minus Ref difference in published TRAP/Input activity, in log2 units.
- ref_shuf_rna_dna_p
- Published nominal p-value for the Ref-versus-Shuf Input-RNA/DNA comparison.
- ref_shuf_rna_dna_fdr
- Published FDR-adjusted p-value for the Ref-versus-Shuf Input-RNA/DNA comparison.
- ref_shuf_rna_dna_bonferroni
- Published Bonferroni-adjusted p-value for the Ref-versus-Shuf Input-RNA/DNA comparison.
- ref_alt_rna_dna_p
- Published nominal p-value for the Ref-versus-Alt Input-RNA/DNA comparison.
- ref_alt_rna_dna_fdr
- Published FDR-adjusted p-value for the Ref-versus-Alt Input-RNA/DNA comparison.
- ref_alt_rna_dna_bonferroni
- Published Bonferroni-adjusted p-value for the Ref-versus-Alt Input-RNA/DNA comparison.
- ref_shuf_trap_input_p
- Published nominal p-value for the Ref-versus-Shuf TRAP/Input comparison.
- ref_shuf_trap_input_fdr
- Published FDR-adjusted p-value for the Ref-versus-Shuf TRAP/Input comparison.
- ref_shuf_trap_input_bonferroni
- Published Bonferroni-adjusted p-value for the Ref-versus-Shuf TRAP/Input comparison.
- ref_alt_trap_input_p
- Published nominal p-value for the Ref-versus-Alt TRAP/Input comparison.
- ref_alt_trap_input_fdr
- Published FDR-adjusted p-value for the Ref-versus-Alt TRAP/Input comparison.
- ref_alt_trap_input_bonferroni
- Published Bonferroni-adjusted p-value for the Ref-versus-Alt TRAP/Input comparison.
Quality control
Author QC was retained: edgeR CPM normalization; barcode measurements with fewer than 10 raw counts in either RNA or DNA were excluded. For in-vitro allele testing, both alleles were required to have at least three barcodes with at least 10 counts in both RNA and DNA in at least four biological replicates; element-wise activities were summarized with a barcode random-intercept mixed model. The table includes only rows with numeric activity in the published Source Data 7 after these filters and excludes known mis-designed alternative elements.
Curation notes
Six replicate N2a Input and six TRAP RNA libraries were paired with six recovered plasmid-DNA libraries. Pairwise log2FC columns use Alt−Ref or Shuf−Ref and are repeated across the element's allele rows; published p/FDR/Bonferroni columns are from Supplementary Data 5/4. modeled_allele_count is the number of allele classes present in the published summary, not the number of biological replicates. The paper cautions that six barcodes may be insufficient for confidently calling rare small allelic effects. Missing auxiliary statistics are preserved as blank values where the published summary did not report them.