Fixed-end N50 5′UTR polysome-profiling MPRA in HepG2
Optimizing 5’UTRs for mRNA-delivered gene editing using deep learningA fixed-end N50 IVT EGFP reporter library with a constant 25-nt 5′ prefix was assayed in HepG2 cells. One biological replicate was fractionated by polysome load and summarized as UTR-level MRL from UMI counts.
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
The unmodified IVT mRNA reporter contained a constant 25-nt 5′ region, a fully randomized 50-nt segment, EGFP CDS, and bovine growth hormone-derived 3′ UTR. Passage-6 HepG2 cells were transfected, lysed after incubation with cycloheximide, fractionated on a sucrose gradient, and sequenced with fraction-specific barcodes and UMIs. MRL is the author-provided mean ribosome load calculated from normalized counts across polysome fractions.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 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 HepG2 replicate.
- mrl_rep1
- Author-calculated mean ribosome load for the HepG2 replicate.
- mrl_mean
- MRL for the single HepG2 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 HepG2 replicate.
- total_umi_min
- Minimum observed total UMI count; identical to total_umi_sum for this single-replicate table.
Quality control
The package follows the authors’ fixed-end comparison workflow: reported UTR strings were truncated to the first 50 nt, and only sequences with total read count >100 in all five fixed-end datasets (two HEK293T replicates, two T-cell replicates, and one HepG2 replicate) were retained. The package additionally required a 50-nt A/C/G/T sequence and finite source MRL values, leaving 204,803 shared UTRs.
Curation notes
The source is GSE232927_processed_defined_end_hepg2_r1.csv.gz. Although HepG2 is often described as hepatocellular carcinoma, Cellosaurus flags the historical classification as problematic; the package retains the GEO/paper label and resolves the biosample to Cellosaurus CVCL:0027. The processed table is restricted to the 204,803-sequence common fixed-end QC set for direct cross-cell comparison.