Experiment / E7X2HMLKD5' UTR / Translation Efficiency MPRA (MPTA)

Random Kozak library NaP-TRAP in zebrafish embryos at 6 hpf

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

A randomized Kozak library varied six nucleotides upstream and one nucleotide downstream of the AUG in a common 3xFLAG-GFP reporter. In vitro transcribed reporter mRNAs were injected into single-cell Danio rerio embryos and translation was measured by NaP-TRAP at 6 hpf.

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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: 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

In vitro transcribed mRNA reporters used a common 3xFLAG-GFP-PEST coding region and 60-adenosine tail. Anti-FLAG immunocapture of nascent peptide complexes was sequenced as pulldown and input; translation is the RPM-normalized pulldown/input ratio.

Processed data

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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

reporter_id: Unique Kozak reporter identifier.
kozak_sequence: 10-nt Kozak insert spanning six randomized upstream bases, AUG, and one randomized downstream base.
insert_sequence: Kozak insert sequence used as the reporter variable region.
sequence_class: Synthetic random-Kozak library label.
input_B1: UMI-deduplicated input count for biological replicate B1.
pulldown_B1: UMI-deduplicated FLAG pulldown count for biological replicate B1.
input_scale_B1: Matched-reporter mapped-read total used for RPM normalization in B1 input.
pulldown_scale_B1: Matched-reporter mapped-read total used for RPM normalization in B1 pulldown.
norm_input_B1: B1 input count divided by input_scale_B1.
norm_pulldown_B1: B1 pulldown count divided by pulldown_scale_B1.
translation_B1: B1 NaP-TRAP translation ratio, norm_pulldown_B1 / norm_input_B1.
input_B2: UMI-deduplicated input count for biological replicate B2.
pulldown_B2: UMI-deduplicated FLAG pulldown count for biological replicate B2.
input_scale_B2: Matched-reporter mapped-read total used for RPM normalization in B2 input.
pulldown_scale_B2: Matched-reporter mapped-read total used for RPM normalization in B2 pulldown.
norm_input_B2: B2 input count divided by input_scale_B2.
norm_pulldown_B2: B2 pulldown count divided by pulldown_scale_B2.
translation_B2: B2 NaP-TRAP translation ratio, norm_pulldown_B2 / norm_input_B2.
input_total: Sum of input counts across B1 and B2.
pulldown_total: Sum of pulldown counts across B1 and B2.
mean_translation: Arithmetic mean of translation_B1 and translation_B2.
sd_translation: Sample standard deviation of replicate translation ratios.
log2_mean_translation: Base-2 logarithm of mean_translation.
n_replicates: Number of replicate translation ratios contributing to the mean.
qc_pass: True for rows retained after the stated reporter and input-read QC filters.

Quality control

ReadKnead trimming/demultiplexing and UMI deduplication were used by the study; UMIs within Hamming distance less than 2 were collapsed. Only exact reporters represented in the Kozak FASTA, with the expected AUG and no indel, were retained. Reporters had to have at least 100 unique input reads in each of the two biological replicates (2,712 reporters retained).

Curation notes

The current data-hub count file contains additional unmatched sequence keys; these were excluded exactly as the published pipeline excludes reporters not found in the library FASTA.

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