A library of 155-nt reference and disease-relevant mutant human 5' UTR fragments fused upstream of EGFP was in vitro transcribed, capped, polyadenylated, and transfected into HEK293T cells. Amplicon sequencing at 30, 75, and 120 minutes quantified RNA decay and mutant/reference half-life differences.
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Organism
Human
Taxonomy ID
NCBITaxon:9606
Biosample
CVCL:0063
Reference genome
GRCh38
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
T7-5' UTR-EGFP RNA reporters were synthesized in vitro, capped with m7G, polyadenylated, and directly delivered with 500 ng RNA per well using Lipofectamine 3000; the study used reporter RNA survival over time as the readout, not polysome profiling or a DNA reporter. Three independent time-course experiments were sampled at 30, 75, and 120 minutes, and amplicon sequencing was used to estimate decay constants and half-lives.
Direct-transfected in vitro-transcribed 5' UTR RNA-stability MPRA: T7-5' UTR-EGFP reporters were capped and polyadenylated, delivered as RNA, and assayed by time-course amplicon sequencing to estimate decay constants and half-lives. It is not a polysome-profiling or ribosome-footprinting translation-efficiency assay.
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 · 22 definitions
element_id
Unique packaged identifier for the tested UTR oligo, formed as variant_id::variant_name.
variant_id
Source locus/strand/reference/alternate identifier from Supplementary file 1 (Mutant column).
variant_name
Source transcript or descriptive variant name.
gene_symbol
Human gene symbol associated with the UTR sequence.
chromosome
Source chromosome label.
start
Source start coordinate for the variant.
stop
Source stop coordinate for the variant.
strand
Source genomic strand.
utr_type
UTR library type; all rows are 5' UTR in this experiment.
reference_allele
Reference allele used in the wild-type reporter.
alternate_allele
Alternate allele used in the mutant reporter.
wild_type_half_life_min
Published wild-type reporter RNA half-life in minutes (t05_WT_HEK).
mutant_half_life_min
Published mutant reporter RNA half-life in minutes (t05_mt_HEK).
half_life_difference_min
Mutant half-life minus wild-type half-life, computed during packaging, in minutes.
mutant_wt_half_life_ratio
Mutant half-life divided by wild-type half-life, computed during packaging.
log2_mutant_wt_half_life_ratio
Log2 of the mutant/wild-type half-life ratio, computed during packaging.
p_value
Published weighted linear regression p-value for the mutant/reference change in decay constant (pval_HEK).
stability_altering
Author-provided yes/no flag for a significant stability change (sig_HEK).
wild_type_gc_fraction
GC fraction of the wild-type UTR sequence.
mutant_gc_fraction
GC fraction of the mutant UTR sequence.
wild_type_ta_fraction
TA dinucleotide ratio of the wild-type UTR sequence.
mutant_ta_fraction
TA dinucleotide ratio of the mutant UTR sequence.
Quality control
The authors removed PCR duplicates (nubeam-dedup for single-end SH-SY5Y data and UMI processing for HEK293T data), trimmed adapters and bases below a sliding mean quality of 20, discarded reads shorter than 80 bp, retained uniquely aligned reads with HISAT2 MAPQ 60, and generated counts with bedtools multicov. For half-life estimation, only oligos with R2 > 0.5 and mean squared error < 1 were retained. The packaged table further retains only records with complete finite paper-reported wild-type and mutant half-lives, p-values, and author-provided stability flags for this cell line/UTR.
Curation notes
Source GEO sample titles: GSM6720977-GSM6720985 (HEK293_5U_1/2/3 at 30, 75, and 120 minutes; three independent experiments). The GEO metadata abbreviates the cell line as HEK293, while the paper's Methods identify authenticated ATCC HEK293T, catalog CRL-11268. The raw GEO matrix contains 6,237 construct rows; the processed table has 1,243 complete QC-passing variant comparisons from the paper's Supplementary file 1. Raw counts are retained unchanged in raw_data/GSE217518_HEK_U5_Raw.csv.gz.