Experiment / E3BYBP38J5' UTR / Translation Efficiency MPRA (MPTA)

Tetramer-repeat validation NaP-TRAP in zebrafish embryos at 6 hpf

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

A synthetic validation library tested all 256 possible tetramer repeats separated by dinucleotide spacers in the common 5'UTR reporter. In vitro transcribed reporters were injected into single-cell zebrafish embryos and translation was measured at 6 hpf.

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: Zebrafish
Taxonomy ID: NCBITaxon:7955
Biosample: UBERON:0000922
Reference genome: Not reported / not applicable
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Each synthetic reporter contains a repeated tetramer motif with dinucleotide spacers, a common Kozak/3xFLAG-GFP-PEST reporter, and poly(A) configuration. Anti-FLAG pulldown and input counts were normalized to five spike-in reporters.

Processed data

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

Visible columns (18 of 18)

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Page 1 · 50 rows · More results available

Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.

Column dictionary · 18 definitions

reporter_id: Synthetic reporter identifier of the form kmer_<tetramer>.
tetramer: Four-nucleotide repeated motif extracted from reporter_id.
insert_sequence: 124-nt synthetic tetramer-repeat insert.
sequence_class: Synthetic tetramer validation label.
input_B1: UMI-deduplicated input count for the single biological replicate.
pulldown_B1: UMI-deduplicated FLAG pulldown count for the single biological replicate.
input_scale_B1: Sum of all five spike-in counts used to normalize input.
pulldown_scale_B1: Sum of all five spike-in counts used to normalize pulldown.
norm_input_B1: Input count divided by input_scale_B1.
norm_pulldown_B1: Pulldown count divided by pulldown_scale_B1.
translation_B1: NaP-TRAP translation ratio, norm_pulldown_B1 / norm_input_B1.
input_total: Input count for the single replicate.
pulldown_total: Pulldown count for the single replicate.
mean_translation: Translation ratio for the single replicate.
sd_translation: Standard deviation; zero because only one replicate is available.
log2_mean_translation: Base-2 logarithm of mean_translation.
n_replicates: Number of replicate translation ratios contributing to the mean (1).
qc_pass: True for rows retained after the input-read QC filter.

Quality control

The study pipeline used UMI deduplication with Hamming distance less than 2 and spike-in normalization. Per the data-hub note, only kmer_ and spike-in reporters were analyzed; the processed table contains the kmer_ reporters only. Reporters with at least 100 unique input reads in the single B1 input run were retained (195 reporters).

Curation notes

The full validation FASTA also contains endogenous validation and uORF reporters, but the data hub explicitly states that only kmer_ and ntrap_spike_ reporters were analyzed. Spike-ins are used for normalization and are not emitted as biological rows.

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