Experiment / E3ZESU73J3' UTR / RNA Stability MPRA (MPRAu)

Known 3′-UTR regulatory motif variants in HEK293 cells

Massively parallel screen uncovers many rare 3′ UTR variants regulating mRNA abundance of cancer driver genes

The C3Sp1 library tested three alternative alleles at positions within five known regulatory motif classes in human 3′ UTRs. Reference and alternative constructs were assayed by episomal MapUTR in HEK293 cells.

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Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:0045
Reference genome: hg19
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Episomal pCAG-eGFP reporter with 200-nt C3Sp1 oligos carrying a 164-nt tested 3′-UTR context. The table contains three DNA and three poly(A) RNA UMI-count replicates and raw RNA/DNA effects calculated per replicate; the HeLa replicate-3 GEO file is a combined C1Sp3/C3Sp1 sample keyed by construct identifier.

Processed data

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Visible columns (37 of 37)

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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 · 37 definitions

element_id: Stable identifier for the tested motif construct
motif: Known 3′-UTR motif class tested
host_gene: Gene providing the tested 3′-UTR context
chromosome: hg19 chromosome
position_hg19: 1-based hg19 position of the mutated motif base
reference_allele: Reference nucleotide inferred as the base not represented among the three alternatives
alternative_allele: Alternative nucleotide in this oligo
gene_strand: Strand of the host gene
oligo_orientation: Design/sequencing orientation (orig or rc)
cell_line: Assayed cell line
paper_avg_relative_score_at_position: Author-provided MOESM9 Fig. 1f average relative score across the three alternative alleles at this position
dna_ref_rep1: Pre-transfection plasmid DNA UMI count for the reference oligo, replicate 1
dna_ref_rep2: Pre-transfection plasmid DNA UMI count for the reference oligo, replicate 2
dna_ref_rep3: Pre-transfection plasmid DNA UMI count for the reference oligo, replicate 3
dna_alt_rep1: Pre-transfection plasmid DNA UMI count for the alternative oligo, replicate 1
dna_alt_rep2: Pre-transfection plasmid DNA UMI count for the alternative oligo, replicate 2
dna_alt_rep3: Pre-transfection plasmid DNA UMI count for the alternative oligo, replicate 3
rna_ref_rep1: Poly(A)-selected reporter RNA UMI count for the reference oligo, replicate 1
rna_ref_rep2: Poly(A)-selected reporter RNA UMI count for the reference oligo, replicate 2
rna_ref_rep3: Poly(A)-selected reporter RNA UMI count for the reference oligo, replicate 3
rna_alt_rep1: Poly(A)-selected reporter RNA UMI count for the alternative oligo, replicate 1
rna_alt_rep2: Poly(A)-selected reporter RNA UMI count for the alternative oligo, replicate 2
rna_alt_rep3: Poly(A)-selected reporter RNA UMI count for the alternative oligo, replicate 3
activity_ref_rep1: Reference RNA/DNA UMI ratio, replicate 1
activity_ref_rep2: Reference RNA/DNA UMI ratio, replicate 2
activity_ref_rep3: Reference RNA/DNA UMI ratio, replicate 3
activity_alt_rep1: Alternative RNA/DNA UMI ratio, replicate 1
activity_alt_rep2: Alternative RNA/DNA UMI ratio, replicate 2
activity_alt_rep3: Alternative RNA/DNA UMI ratio, replicate 3
raw_log2fc_rep1: Raw log2 alternative/reference activity ratio, replicate 1
raw_log2fc_rep2: Raw log2 alternative/reference activity ratio, replicate 2
raw_log2fc_rep3: Raw log2 alternative/reference activity ratio, replicate 3
raw_mean_log2fc_alt_vs_ref: Mean raw log2 alternative/reference activity ratio across available replicates
raw_activity_fold_change_alt_vs_ref: 2 raised to the raw mean log2 activity ratio
raw_activity_percent_change: 100 times (raw activity fold change minus 1)
qc_pass: True when all 12 DNA/RNA UMI counts for both alleles met the minimum-count filter
qc_exclusion_reason: Reason for exclusion; blank for retained rows

Quality control

The authors removed reads with more than one mismatch, or a mismatch at the designed SNP, deduplicated PCR products using 15-mer UMIs, and quantified UMI counts after alignment. For this table, rows were retained only when both alleles had UMI counts of at least 10 in all three DNA and RNA replicates (905/905 rows). Extra records co-packaged in the combined HeLa replicate-3 file that were not part of the C3Sp1 design were excluded.

Curation notes

The five motif groups represented in the deposited C3Sp1 design are SAMD4A, ARE, hPUM, dPUM, and CDE; the raw label sRSM1,CDE is normalized to CDE. The position-level score annotation is author-provided from MOESM9 Fig. 1f; activity effects are recomputed from deposited UMI counts.

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