Experiment / E5TPZ01BX5' UTR / Translation Efficiency MPRA (MPTA)

Zebrafish 5'UTR library polysome profiling in HEK293T cells at 12 hpt

NaP-TRAP reveals the regulatory grammar in 5’UTR-mediated translation regulation during zebrafish development

The zebrafish 5'UTR tiled reporter library was transfected into HEK293T cells and fractionated by sucrose-gradient polysome profiling 12 hours post-transfection. The table reconstructs the reporter-level fraction distributions and mean ribosome load (MRL) used to benchmark NaP-TRAP.

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: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

HEK293T cells received in vitro transcribed zebrafish 5'UTR reporters and were fractionated after cycloheximide arrest. Each reporter's count was normalized within fraction, renormalized across the 13 analyzed fractions, and weighted by the reported ribosome-load labels (r1 through r11) to calculate MRL.

Processed data

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

Visible columns (28 of 28)

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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 · 28 definitions

reporter_id: Source reporter identifier, generally a zebrafish transcript tile ID.
insert_sequence: 124-nt tiled zebrafish 5'UTR or named IRES variable sequence.
source_transcript: Transcript or named IRES source parsed from reporter_id.
tile_index: Tile number parsed from the final numeric suffix of reporter_id; blank for non-tiled names.
sequence_class: Reporter source classification.
r1_raw_count: Raw count summed over analyzed physical fractions assigned to r1.
r1_fraction: Reporter-normalized read share in r1.
r2_raw_count: Raw count summed over analyzed physical fractions assigned to r2.
r2_fraction: Reporter-normalized read share in r2.
r3_raw_count: Raw count summed over analyzed physical fractions assigned to r3.
r3_fraction: Reporter-normalized read share in r3.
r4_raw_count: Raw count in the analyzed physical fraction assigned to r4.
r4_fraction: Reporter-normalized read share in r4.
r5_raw_count: Raw count summed over analyzed physical fractions assigned to r5.
r5_fraction: Reporter-normalized read share in r5.
r6.5_raw_count: Raw count in the analyzed physical fraction assigned to r6.5.
r6.5_fraction: Reporter-normalized read share in r6.5.
r7.5_raw_count: Raw count in the analyzed physical fraction assigned to r7.5.
r7.5_fraction: Reporter-normalized read share in r7.5.
r9_raw_count: Raw count in the analyzed physical fraction assigned to r9.
r9_fraction: Reporter-normalized read share in r9.
r11_raw_count: Raw count in the analyzed physical fraction assigned to r11.
r11_fraction: Reporter-normalized read share in r11.
mrl: Mean ribosome load, the sum of each fraction share multiplied by its ribosome-load label.
total_reads_all_fractions: Reporter raw counts summed across all 14 archived fraction runs, including excluded Fraction 26.
total_reads_used_fractions: Reporter raw counts summed across the 13 fractions used for MRL.
n_analyzed_fractions: Number of physical fraction runs used for MRL (13).
qc_pass: True for reporters present in all 13 analyzed fractions.

Quality control

The published MRL calculation retained 9,531 biological reporter entries present in every one of the 13 analyzed fractions (Fractions 11, 12, and 15-25). Spike-ins were excluded from the table. Fraction 26 (AGR004823) is retained in raw_data but excluded from MRL because it is absent from the published configuration and supplementary MRL table.

Curation notes

The data hub lists AGR004823 as Fraction 26, but the repository build configuration omits it and the supplied MRL workbook has 13 physical fractions grouped as r1, r2, r3, r4, r5, r6.5, r7.5, r9, and r11. The package follows that published convention. Assay organism is human HEK293T; inserts derive from zebrafish transcript 5'UTRs.

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