Experiment / E8XG57HDI5' UTR / Translation Efficiency MPRA (MPTA)

Zebrafish 5'UTR library NaP-TRAP 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 translation was measured 12 hours post-transfection by NaP-TRAP. The table reports reporter-level FLAG pulldown/input translation effects across four biological replicates.

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

In vitro transcribed zebrafish 5'UTR reporters were transfected with Lipofectamine MessengerMAX into HEK293T cells. Translation was measured by anti-FLAG nascent-chain immunocapture at 12 hpt; counts were RPM-normalized because no spike-in scaling was specified for the HEK293T NaP-TRAP run.

Processed data

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

Visible columns (40 of 40)

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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 · 40 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.
input_B1: UMI-deduplicated HEK293T 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 HEK293T 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_B3: UMI-deduplicated HEK293T input count for biological replicate B3.
pulldown_B3: UMI-deduplicated FLAG pulldown count for biological replicate B3.
input_scale_B3: Matched-reporter mapped-read total used for RPM normalization in B3 input.
pulldown_scale_B3: Matched-reporter mapped-read total used for RPM normalization in B3 pulldown.
norm_input_B3: B3 input count divided by input_scale_B3.
norm_pulldown_B3: B3 pulldown count divided by pulldown_scale_B3.
translation_B3: B3 NaP-TRAP translation ratio, norm_pulldown_B3 / norm_input_B3.
input_B4: UMI-deduplicated HEK293T input count for biological replicate B4.
pulldown_B4: UMI-deduplicated FLAG pulldown count for biological replicate B4.
input_scale_B4: Matched-reporter mapped-read total used for RPM normalization in B4 input.
pulldown_scale_B4: Matched-reporter mapped-read total used for RPM normalization in B4 pulldown.
norm_input_B4: B4 input count divided by input_scale_B4.
norm_pulldown_B4: B4 pulldown count divided by pulldown_scale_B4.
translation_B4: B4 NaP-TRAP translation ratio, norm_pulldown_B4 / norm_input_B4.
input_total: Sum of input counts across B1-B4.
pulldown_total: Sum of pulldown counts across B1-B4.
mean_translation: Arithmetic mean of the four 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. Only reporters with at least 100 unique input reads in each of four biological replicates were retained (7,584 reporters).

Curation notes

The assay organism is human HEK293T, but the reporter inserts are zebrafish transcript 5'UTR tiles; the sequence source is therefore retained explicitly in the table.

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