Fixed-end N50 5′UTR polysome-profiling MPRA in HEK293T
Optimizing 5’UTRs for mRNA-delivered gene editing using deep learningA pooled in-vitro-transcribed EGFP reporter library with a constant 25-nt 5′ prefix and a fully randomized 50-nt 5′UTR segment was profiled in HEK293T cells. Two biological replicates were fractionated by polysome load, and sequence-level mean ribosome load (MRL) was calculated 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 reporter was unmodified IVT mRNA containing a fixed 25-nt 5′ region, a randomized 50-nt region, EGFP CDS, and a bovine growth hormone-derived 3′ UTR. HEK293T cells were transfected, lysed after the library incubation period in cycloheximide, separated on a sucrose gradient, and fraction-specific barcodes/UMIs were sequenced. MRL is the author-provided ribosome-load score derived 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 · 13 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 HEK293T replicate 1.
- mrl_rep1
- Author-calculated mean ribosome load for HEK293T replicate 1.
- total_umi_rep2
- Sum of processed UMI counts across all polysome fractions in HEK293T replicate 2.
- mrl_rep2
- Author-calculated mean ribosome load for HEK293T replicate 2.
- mrl_mean
- Arithmetic mean of the replicate MRL values.
- mrl_sd
- Sample standard deviation of replicate MRL values.
- mrl_weighted_mean
- Total-UMI-weighted mean of replicate MRL values.
- total_umi_sum
- Sum of total UMI counts across the packaged biological replicates.
- total_umi_min
- Minimum total UMI count across the packaged biological replicates.
Quality control
The package follows the authors’ analysis workflow: each source table was truncated to the first 50 nt of the reported UTR field, and sequences with a total read count >100 in every one of the two HEK293T, two T-cell, and one HepG2 fixed-end datasets were retained. The package additionally required a 50-nt A/C/G/T sequence and finite source MRL values. The resulting shared QC set contains 204,803 UTRs; rows failing coverage or sequence/QC checks were excluded.
Curation notes
The HEK293T fixed-end measurements were generated in the prior GSE114002 study and reused here as the HEK293T comparator/training data. GSM3130436 reports the UTR plus the constant suffix ATGGGCGAA; the package uses the first 50 nt, matching the current paper’s published analysis code. Source polysome-fraction UMI tables remain in raw_data; the processed table retains replicate totals and MRL effect scores rather than raw reads. HEK293T was resolved to Cellosaurus CVCL:0063.