PC3 small PLUMAGE 8-bp barcode proof-of-principle
Multiplexed functional genomic analysis of 5′ untranslated region mutations across the spectrum of prostate cancerA small episomal PLUMAGE library tested full-length wild-type and mutant 5′-UTRs from ADAM32, COMT, and ZCCHC7 in PC3 cells. Each construct was linked to five known 8-bp barcodes; the packaged table combines PacBio construct-linkage counts with the published transcript and translation-efficiency summaries and pilot replicate values.
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
Basal / Untreated (24 h post-transfection)
Episomal pGL3-promoter luciferase reporter constructs carried full-length human 5′-UTRs and a fixed, known 8-bp barcode cloned at the 3′ end of the luciferase coding sequence. The pooled library was transfected into PC3 cells; DNA, total mRNA, and polysome-bound mRNA were sequenced, and translation efficiency was measured as normalized polysome signal relative to normalized total-RNA signal.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (28 of 28)
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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 · 28 definitions
- variant_id
- Stable variant identifier using the gene, hg19 chromosome, position, reference allele, and alternative allele.
- gene
- Gene symbol for the assayed 5′-UTR.
- variant_position_hg19
- hg19 genomic position of the tested 5′-UTR mutation.
- reference_allele
- Reference nucleotide at the tested position.
- alternative_allele
- Mutant nucleotide at the tested position.
- cell_line
- Cell line used for the pilot assay.
- barcode_design
- Description of the fixed barcode design and its relationship to the WT and mutant constructs.
- wild_type_barcodes
- Semicolon-separated known 8-bp barcodes assigned to the WT construct.
- mutant_barcodes
- Semicolon-separated known 8-bp barcodes assigned to the mutant construct.
- wild_type_barcode_count
- Number of WT barcodes retained in the table.
- mutant_barcode_count
- Number of mutant barcodes retained in the table.
- wild_type_total_long_read_count
- Sum of author-reported PacBio long-read counts across WT barcodes.
- mutant_total_long_read_count
- Sum of author-reported PacBio long-read counts across mutant barcodes.
- wild_type_mean_long_read_count
- Mean author-reported PacBio long-read count per WT barcode.
- mutant_mean_long_read_count
- Mean author-reported PacBio long-read count per mutant barcode.
- wild_type_translation_efficiency_replicates
- Semicolon-separated pilot normalized polysome/total-RNA values for individual WT barcodes from Source Data Figure 1g.
- mutant_translation_efficiency_replicates
- Semicolon-separated pilot normalized polysome/total-RNA values for individual mutant barcodes from Source Data Figure 1g.
- transcript_log2_fold_change
- Published log2 fold change for mutant versus WT transcript activity from the PLUMAGE summary.
- transcript_p_value
- Published two-sided Mann–Whitney U-test p-value for the transcript comparison.
- transcript_fdr
- Published FDR-adjusted p-value for the transcript comparison.
- transcript_significant_fdr_lt_0_1
- Whether the published transcript FDR is below 0.1.
- translation_efficiency_log2_fold_change
- Published log2 fold change for mutant versus WT translation efficiency; blank means no corresponding row was supplied in Supplementary Data 6e.
- translation_efficiency_p_value
- Published p-value for the translation-efficiency comparison; blank means unavailable in the supplied summary.
- translation_efficiency_fdr
- Published FDR-adjusted p-value for the translation-efficiency comparison; blank means unavailable in the supplied summary.
- translation_efficiency_significant_fdr_lt_0_1
- Whether the published translation-efficiency FDR is below 0.1; false when no published summary row is available.
- functional_in_any_layer
- Whether the published FDR is below 0.1 in either the transcript or translation-efficiency layer.
- qc_pass
- Package-level QC flag; only true rows are present in the processed table.
- source_data
- Supplementary workbooks and source-data sheet used to construct the row.
Quality control
The paper reports that all 30 pilot 8-bp barcodes were detected and linked to their expected full-length WT or mutant 5′-UTR by long-read sequencing. For this package, a row passed QC only when both alleles had exactly five unique barcodes and every packaged long-read count was positive; all three variant pairs passed, so no candidate row was removed. Published FDR values are retained as effect annotations rather than used to discard nonsignificant variants.
Curation notes
PC3 corresponds to Cellosaurus CVCL:0035. Supplementary Data 6e does not provide a ZCCHC7_MUT_8mer effect-summary row, so its translation-efficiency summary fields are blank rather than treated as zero or nonsignificant; the available ZCCHC7 pilot replicate values from Source Data Figure 1g are retained. The five-barcode counts are construct-linkage/long-read counts and should not be interpreted as RNA/DNA activity measurements.