eGFP random 50-mer library, unmodified uridine
Human 5′ UTR design and variant effect prediction from a massively parallel translation assayDuplicate polysome-profiling measurements of a 280,000-member random 50-nt 5′-UTR library in a constant eGFP reporter context using unmodified IVT mRNA in HEK293T cells. The processed table contains sequence-supported replicate MRLs and a derived two-replicate mean.
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
Unmodified uridine (U) IVT mRNA
HEK293T cells were transfected with in-vitro-transcribed reporter mRNA; cells were harvested 12 h later, polysome fractions were collected, fraction-associated sequences were quantified by barcode/NGS, and Mean Ribosome Load (MRL) was computed from relative fraction distributions. The reporter used a defined 25-nt leader and constant eGFP CDS/3′ context; this is an RNA polysome-profiling MPTA rather than a DNA plasmid MPRA. GEO samples GSM3130435 and GSM3130436 are the two biological replicates.
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 · 12 definitions
- element_id_rep1
- Raw GEO row identifier for the first biological replicate.
- element_id_rep2
- Raw GEO row identifier for the second biological replicate.
- utr_sequence
- Uppercase tested 5′-UTR insert sequence; fixed reporter CDS overlap removed where present.
- utr_length
- Length of the cleaned 5′-UTR insert in nucleotides.
- uaug_count
- Number of ATG motifs in the cleaned insert; reading frame is not inferred.
- coverage_metric_rep1
- GEO-provided per-element coverage metric used for within-replicate ranking; source field is total_reads when available and otherwise total.
- coverage_metric_rep2
- GEO-provided per-element coverage metric used for within-replicate ranking; source field is total_reads when available and otherwise total.
- mrl_rep1
- Published mean ribosome load (MRL) for replicate 1.
- mrl_rep2
- Published mean ribosome load (MRL) for replicate 2.
- mrl_mean
- Arithmetic mean of the two published replicate MRL values.
- mrl_sd
- Sample standard deviation of the two replicate MRL values.
- mrl_delta_rep2_minus_rep1
- Replicate 2 MRL minus replicate 1 MRL.
Quality control
Applied the authors’ sequence-processing rule: valid reporter sequence and the top 280,000 eGFP members ranked by the GEO-provided coverage field per replicate. For this generated table, additionally required A/C/G/T sequence, an expected 50-nt insert, positive finite coverage metric and finite MRL in both replicates, collapsed duplicate cleaned sequences to the highest-coverage row, and retained only sequences observed in both QC-passed replicates (271,648 rows). The raw GEO fraction fields remain in GSE114002_RAW.tar.
Curation notes
The two GEO files use different fraction-header conventions; the second includes a fixed 9-nt eGFP CDS overlap in its sequence field, which was removed to harmonize the 50-nt insert. coverage_metric_rep1 is total_reads while coverage_metric_rep2 is total; the latter is a GEO count field for this condition. Primary assay values are mrl_rep1 and mrl_rep2; mrl_mean, mrl_sd, and mrl_delta_rep2_minus_rep1 are generated summaries. The raw ten-file archive is retained.