Experiment / E1KHDK1N25' UTR / Translation Efficiency MPRA (MPTA)

Random-end N50 5′UTR polysome-profiling MPRA in HEK293T

Optimizing 5’UTRs for mRNA-delivered gene editing using deep learning

A HEK293T IVT EGFP reporter library with a 50-nt fully randomized 5′UTR and only the T7-compatible 5′ guanine prefix was profiled in one biological replicate. UTR-level MRL values were retained with total UMI coverage after polysome fractionation.

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Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:0063
Reference genome: Not reported / not applicable
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

The random-end construct used a 50-nt variable 5′UTR downstream of the T7-derived guanine prefix, followed by EGFP and the reporter 3′ UTR. HEK293T cells were transfected and subjected to cycloheximide-stabilized sucrose-gradient polysome profiling. Reverse transcription/template switching introduced UMIs; fraction-specific libraries were sequenced and MRL was calculated from normalized UMI counts.

Processed data

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

Visible columns (11 of 11)

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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 · 11 definitions

element_id: Stable package identifier assigned in lexicographic UTR-sequence order after QC.
utr_sequence: The variable 50-nt random-end 5′UTR sequence represented by the reporter library.
utr_length: Length of the packaged variable UTR sequence in nucleotides.
replicate_count: Number of biological replicates with a finite MRL value for the sequence.
total_umi_rep1: Sum of processed UMI counts across all polysome fractions in the random-end N50 replicate.
mrl_rep1: Author-calculated mean ribosome load for the random-end N50 replicate.
mrl_mean: MRL for the single HEK293T biological replicate.
mrl_sd: Blank because only one biological replicate is available.
mrl_weighted_mean: Total-UMI-weighted MRL; identical to the single-replicate MRL here.
total_umi_sum: Total UMI count in the packaged random-end N50 replicate.
total_umi_min: Minimum observed total UMI count; identical to total_umi_sum for this single-replicate table.

Quality control

The author analysis retained one-replicate sequences with total UMI coverage ≥100. The package additionally required an exact 50-nt A/C/G/T sequence and finite source MRL values, leaving 148,689 UTRs; lower-coverage rows were excluded.

Curation notes

The source is GSE232927_processed_random_end_hek293t_N50_r1.csv.gz. The exact GEO file yields 148,689 sequences at the documented ≥100-UMI threshold, consistent with the paper’s approximately 149k report. HEK293T was resolved to Cellosaurus CVCL:0063.

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