Experiment / E4VCFCTDP5' UTR / Translation Efficiency MPRA (MPTA)

Zebrafish 5'UTR NaP-TRAP at 6 hpf with SV40 polyadenylation signal

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

A 124-nt library tiled the 5'UTRs of maternally supplied zebrafish transcripts plus IRES controls. The in vitro transcribed library was injected into single-cell embryos and translation was measured at 6 hpf using the SV40 reporter 3' processing configuration.

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

Perturbation & assay details

Basal / Untreated

In vitro transcribed 5'UTR mRNA reporters used a common Kozak/3xFLAG-GFP-PEST reporter with an SV40 polyadenylation signal. Anti-FLAG nascent-chain pulldown and input counts were normalized to spike-in reporters; ntrap_spike_3 was excluded as specified by the paper.

Processed data

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

Visible columns (26 of 26)

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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 · 26 definitions

reporter_id: Source reporter identifier, generally a transcript tile ID.
insert_sequence: 124-nt tiled 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.
input_B1: UMI-deduplicated input count for biological replicate B1.
pulldown_B1: UMI-deduplicated FLAG pulldown count for biological replicate B1.
input_scale_B1: Sum of retained spike-in counts used to normalize B1 input.
pulldown_scale_B1: Sum of retained spike-in counts used to normalize 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: Sum of retained spike-in counts used to normalize B2 input.
pulldown_scale_B2: Sum of retained spike-in counts used to normalize 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 the two replicate translation ratios.
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 input-read QC.

Quality control

ReadKnead/Bowtie2 mapping and UMI deduplication were used by the study, with UMIs within Hamming distance less than 2 collapsed. Counts were spike-normalized after excluding ntrap_spike_3. Only reporters with at least 100 unique input reads in each of B1 and B2 were retained (7,442 reporters).

Curation notes

The data-hub run table repeats the poly(A) run IDs for its SV40 rows; this package uses the distinct SV40 mapping from the repository configuration and supplied processed workbook: AGR003835/AGR003836 input and AGR003839/AGR003840 pulldown.

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