Experiment / E60VYYIV35' UTR / Translation Efficiency MPRA (MPTA)

mCherry random 50-mer library, unmodified uridine

Human 5′ UTR design and variant effect prediction from a massively parallel translation assay

Duplicate polysome-profiling measurements of a random 50-nt 5′-UTR library in a constant mCherry reporter context using unmodified IVT mRNA in HEK293T cells. The processed table contains sequence-supported replicate MRLs and a derived two-replicate mean.

Download processed table (CSV)Raw source data API documentation

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.

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

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 mCherry CDS/3′ context; this is an RNA polysome-profiling MPTA rather than a DNA plasmid MPRA. GEO samples GSM3130441 and GSM3130442 are the two biological replicates.

Processed data

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

Visible columns (12 of 12)

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Page 1 · 50 rows · More results available

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.
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.
coverage_metric_rep2: GEO-provided per-element coverage metric used for within-replicate ranking; source field is 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 200,000 mCherry 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 (173,445 rows). The raw GEO fraction fields remain in GSE114002_RAW.tar.

Curation notes

The two mCherry replicates have different fraction counts but no fixed eGFP CDS suffix; source MRLs were retained unchanged and the simple mean/SD/delta columns are derived. The raw GEO fraction fields remain available in the retained archive.

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