Duplicate polysome-profiling measurements of a 280,000-member random 50-nt 5′-UTR library in a constant eGFP reporter context using pseudouridine-substituted 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.
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
Pseudouridine (Ψ) substituted for uridine in 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 GSM3130437 and GSM3130438 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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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.
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 for this experiment.
coverage_metric_rep2
GEO-provided per-element coverage metric used for within-replicate ranking; source field is total for this experiment.
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 (270,130 rows). The raw GEO fraction fields remain in GSE114002_RAW.tar.
Curation notes
Both replicate GEO files contain the fixed 9-nt eGFP CDS overlap and extra alternate r columns; processing removed only the known overlap and reported the source rl measurement unchanged. The source total field is normalized signal in these files, so coverage_metric_rep1/2 should not be treated as integer read counts. Primary assay values are mrl_rep1 and mrl_rep2; the other MRL columns are generated summaries.