A highly overlapping library of sonicated zebrafish maternal 3′-UTR fragments was placed in a common GFP reporter, transcribed in vitro, and injected into one-cell embryos. RNA-seq coverage at 2 hpf and 8 hpf, with a parallel 430LNA miR-430-inhibition control, was used to call mRNA-destabilizing and stability-promoting regions.
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
Zv9
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Developmental transition from 2 hpf to 8 hpf; parallel 1 nL of 10 μM 430LNA treatment to inhibit miR-430
RESA is an RNA reporter MPRA with an in-vitro-transcribed library rather than a plasmid-DNA activity readout. Approximately 56-129 nt fragments from 434 maternal zebrafish 3′UTRs were inserted into the 3′UTR of a common GFP open reading frame with an SP6 promoter and SV40 polyadenylation signal; 10 pg library RNA was injected into one-cell embryos. Sense paired-end fragments between 56 and 129 nt were counted by UTR position, normalized to total positional counts with a 0.5 smoothing factor, and compared between early and late stages. 430LNA was used to separate miR-430-dependent from independent regulation.
Processed data
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Visible columns (14 of 14)
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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 · 14 definitions
element_id
Stable package identifier combining the source UTR, Zv9 interval, and UTR-relative critical point.
utr_id
Ensembl zebrafish UTR/library identifier from Supplementary Data 3.
gene_symbol
Gene symbol suffix parsed from the source UTR identifier.
regulation
Published direction of the responsive region: DESTABILIZING or STABILIZING.
coordinate_zv9
Broad genomic interval of the responsive region on the zebrafish Zv9 assembly.
critical_point_utr
UTR-relative position of the local coverage-ratio minimum or maximum used to center the call.
log2_late_vs_early
Published log2 positional coverage ratio for late (8 hpf) versus early (2 hpf) embryos.
late_vs_early_fold_change
Derived late/early coverage fold change, calculated as 2 raised to log2_late_vs_early.
width_nt
Width of the called responsive region in nucleotides.
coverage
Published positional coverage value at the critical point.
prediction
Published regulatory classification, including MIR430, NON-MIR430, BOTH_ADJACENT, or blank where unclassified.
base_dependencies
Published dependence on C/G bases for RESA-Bisulfite follow-up, or blank when not assigned.
confidence
Published region-call confidence; all processed rows are HIGH.
source_table
Supplementary table from which the row was derived.
Quality control
The authors trimmed Illumina adapters, aligned reads to a masked zebrafish Zv9 reference with TopHat and amplicon-specific transcript definitions, kept sense fragments of 56-129 nt, and excluded UTRs with zero median pooled early-stage coverage. Their region-calling rules used local coverage-ratio minima/maxima; high-confidence calls require the published high-confidence width, coverage, and effect thresholds. Package QC retained 787 of 1,850 Supplementary Data 3 rows: rows had to be marked HIGH, have finite required numeric fields, width >= 65 nt, and coverage >= 100X. The 1,063 LOW-confidence calls are left in raw_data but excluded from the processed table.
Curation notes
The source library spans 434 maternal 3′UTRs and 502,728 nucleotides; coordinates are on zebrafish Zv9. Supplementary Data 3 combines destabilizing and stabilizing calls and includes both high- and low-confidence results. The processed table intentionally preserves the published high-confidence calls only, including both directions of regulation. Blank prediction/base_dependencies cells correspond to the source table's '.' placeholder. The experiment is classified as MPRAu because the tested 3′UTR sequences are assayed in a common reporter RNA and the primary readout is RNA stability/differential accumulation.