Experiment / E77V5Q6JJ3' UTR / RNA Stability MPRA (MPRAu)

PERSIST-seq pooled mRNA in-solution stability time course

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

The 233-member synthetic mRNA pool was subjected to accelerated in-solution degradation and sampled over ten time points; intact full-length molecules were quantified by barcode sequencing. Exponential fits provide construct-specific degradation coefficients and half-lives.

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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: Not reported
Taxonomy ID: Not reported / not applicable
Biosample: Not reported / not applicable
Reference genome: Not reported / not applicable
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

50 mM Na-CHES, pH 10.0, 10 mM MgCl2, approximately 24–25°C

This PERSIST-seq arm is an in-solution barcode-sequencing readout rather than a cellular biosample: uncapped, non-polyadenylated pooled mRNAs were incubated in degradation buffer at 0, 0.5, 1, 2, 3, 4, 5, 6, 16, and 24 hours. Intact full-length RT-PCR products were counted by barcode sequencing and fit to an exponential fraction-intact model. The input library is entirely synthetic, so no organism, genome assembly, or genomic region is assigned.

Processed data

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

Visible columns (21 of 21)

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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 · 21 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_solution_degradation_coefficient_per_hour: In-solution mRNA degradation coefficient per hour from the author’s exponential fit of the fraction of intact RNA.
in_solution_degradation_coefficient_error_per_hour: Author-reported error estimate for the in-solution degradation coefficient.
in_solution_half_life_hours: In-solution mRNA half-life in hours, calculated from the exponential-fit time constant.
qc_pass: TRUE for a construct retained after modality-specific QC and finite-value filtering.

Quality control

The author’s in-solution processing rejects time courses whose final observed fraction intact exceeds the fitted exponential by more than 0.05, indicating likely misprimed non-full-length amplification. The supplied author table has complete finite in-solution coefficient, error, and half-life values for 191 of 233 constructs; the other 42 were omitted here and no values were imputed.

Curation notes

This is the in-solution stability arm of PERSIST-seq. It is included because it is a genuine pooled barcode reporter readout of the same designed mRNA variants, but it has no biological cell or tissue biosample.

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