Experiment / E4J3UM3JE5' UTR / Translation Efficiency MPRA (MPTA)

PERSIST-seq pooled mRNA polysome profiling

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

A 233-member library of full-length, in-vitro-transcribed reporter mRNAs with unique 3′-UTR barcodes was transfected into HEK293T cells and separated by sucrose-gradient polysome profiling. Barcode sequencing across the fractions quantifies construct-specific translation/ribosome loading.

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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: 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 rather than plasmid or viral DNA delivery. The 233 full-length constructs vary 5′ UTRs, 3′ UTRs, and CDSs; each carries a 6–9-nt barcode in the 3′ UTR. RNA barcode counts from sucrose fractions were UMI-deduplicated, log-transformed, normalized by a spike-in linear fit, and combined with the published fraction-weight vector to calculate ribosome_load.

Processed data

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

Visible columns (23 of 23)

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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 · 23 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).
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.
monosome_to_40s60s_ratio: Normalized fraction-4 (80S monosome) abundance divided by the 40S/60S abundance.
polysome_to_monosome_ratio: Normalized summed polysome fraction abundance divided by monosome abundance.
polysome_to_40s60s_ratio: Normalized polysome abundance divided by 40S/60S abundance.
qc_pass: TRUE for a construct retained after modality-specific QC and finite-value filtering.

Quality control

The source pipeline trims constant regions, aligns reads to the barcode reference, deduplicates UMIs, log-transforms and spike-in normalizes sample columns, and calculates relative fraction abundance. All 233 constructs had finite ribosome_load and ribosome_load_error values in the supplied author analysis; all were retained. No genomic-coordinate filter applies because the library is synthetic.

Curation notes

This is a pooled RNA-transfection reporter assay and is therefore annotated as an MPTA-style translation-efficiency MPRA. The table contains construct-level polysome outputs; the barcode-by-sample count matrix and barcode reference are retained in raw_data for reanalysis. The library is synthetic and has no reference genome or continuous genomic region.

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