Experiment / E7AEY4JHC3' UTR / RNA Stability MPRA (MPRAu)

PERSIST-seq pooled mRNA in-cell stability time course

Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

The same 233 full-length barcoded reporter mRNAs were transfected into HEK293T cells, harvested over the in-cell time course, and quantified by full-length RT-PCR followed by barcode sequencing. The resulting normalized abundance trajectories quantify construct-specific mRNA decay and half-life.

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

Basal / Untreated

PERSIST-seq uses pooled m7G-capped, poly(A)-tailed synthetic mRNAs with a barcode in the 3′ UTR. A first RT-PCR spans the full CDS to select intact transcripts before a second barcode amplicon; the author analysis fits normalized log RNA abundance over time and reports degradation_coef_in_cell, half_life_in_cell, and a model-predicted protein output that combines stability with ribosome load. The author script uses the early 1-, 7-, and 12-hour points for the stability fit.

Processed data

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

Visible columns (25 of 25)

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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 · 25 definitions

element_id: Unique construct identifier from the authors’ pooled 233-sequence library.
construct_name: Human-readable construct/design name supplied by the authors.
library_group: Author-defined library category, such as UTR or CDS variants.
utr5_description: Description or source label for the tested 5′ UTR.
cds_description: Description or source label for the tested coding sequence.
utr3_description: Description or source label for the tested 3′ UTR.
utr5_type: Author annotation for the 5′ UTR origin/type (for example cellular, viral, or others).
cds_type: Author annotation for the CDS design type (for example start or design).
utr3_type: Author annotation for the 3′ UTR origin/type.
rna_sequence: Full synthetic reporter RNA sequence in the author annotation, including UTRs, CDS, barcode/constant regions, and flanking sequence as provided.
rna_length: Length of rna_sequence in nucleotides.
utr5_sequence: Parsed 5′ UTR nucleotide sequence in RNA alphabet.
cds_sequence: Parsed CDS nucleotide sequence when available; blank where the source annotation did not provide a parsed segment.
cds_sequence_longest: Longest CDS sequence parsed by the authors; retained because some constructs have a blank cds_sequence field.
barcode_sequence: Sequence barcode embedded in the reporter 3′ UTR and counted by short-read sequencing.
utr3_sequence: Parsed 3′ UTR nucleotide sequence in RNA alphabet when available.
long_amplicon_flag: Author processing flag indicating whether the construct was assigned to the long-amplicon class (TRUE/FALSE).
in_cell_degradation_coefficient_per_hour: Positive in-cell mRNA degradation coefficient per hour from the author’s linear fit of normalized log RNA abundance over time.
in_cell_degradation_coefficient_error_per_hour: Author-reported error estimate for the in-cell degradation coefficient.
in_cell_half_life_hours: In-cell mRNA half-life in hours, calculated from the degradation coefficient.
predicted_expression: Model-predicted protein output from the combined in-cell stability and ribosome-load measurements; arbitrary units.
predicted_expression_error: Author-reported error estimate for predicted_expression.
ribosome_load: Weighted mean ribosome load derived from normalized RNA abundance across the sucrose-gradient fractions.
ribosome_load_error: Author-reported error estimate for ribosome_load.
qc_pass: TRUE for a construct retained after modality-specific QC and finite-value filtering.

Quality control

The processed author table reports finite in-cell degradation coefficient, coefficient error, half-life, predicted expression, and predicted-expression error for 203 of 233 constructs. Rows lacking the in-cell fit were omitted from this experiment table; no values were imputed. Rows retained here pass the author’s source analysis and all required modality fields are finite.

Curation notes

The 203 retained constructs are the subset with a complete author-reported in-cell fit. The remaining 30 constructs remain represented in the translation table and in raw_data, but are omitted here rather than given synthetic decay values.

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