The RESA-Bisulfite library was generated from the same zebrafish 3′-UTR fragment pool after partial bisulfite conversion, producing C→U or G→A substitutions across individual reporter molecules. Comparing wild-type and converted-base representation between 2 hpf and 8 hpf embryos identified nucleotide positions and linked bases required for mRNA destabilization or stabilization.
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
RESA-Bisulfite C→U/G→A mutagenesis across the reporter library; developmental transition from 2 hpf to 8 hpf
The same in-vitro-transcribed GFP-3′UTR reporter design was used after bisulfite treatment. Partially converted library molecules were injected into one-cell zebrafish embryos; the observed C/G conversion rate was approximately 68%. Reads were aligned to C→T- and G→A-converted reference representations, wild-type and converted base counts were enumerated at informative positions, and late-versus-early differences were assessed with G tests of independence and Benjamini-Hochberg correction. Linked consecutive-but-not-necessarily-adjacent C or G bases were also analyzed as multi-base events.
Processed data
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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.
Ensembl zebrafish UTR/library identifier from Supplementary Data 4.
gene_symbol
Gene symbol suffix parsed from the source UTR identifier.
effect
Published event class: WT_DEPLETED or MUT_DEPLETED in the late-versus-early comparison.
wt_base
Reference wild-type C or G base interrogated by bisulfite conversion.
converted_base
Expected converted base derived from wt_base: C→T or G→A.
n_linked_bases
Number of linked C/G bases included in the event test.
relative_positions
UTR-relative position or comma-separated positions of the tested base event(s).
coordinate_zv9
Zebrafish Zv9 genomic coordinate or interval for the event.
strand
Source strand orientation for the event coordinate.
log2_late_vs_early_wt_proportion
Published log2 ratio of the wild-type-base proportion in late versus early embryos.
late_vs_early_wt_proportion_fold_change
Derived late/early wild-type proportion fold change, calculated as 2 raised to the published log2 score.
g_statistic
G statistic from the source test of independence.
p_value
Unadjusted p-value for the source G test.
p_adjusted
Benjamini-Hochberg adjusted p-value from the source table.
significant_fdr_0_05
Boolean indicating the source adjusted p-value is <= 0.05; true for every packaged row.
sequence_context
Source sequence context around the event, preserving the source capitalization convention.
overlapping_region
Published RESA region class overlapped by the event, or blank when none was assigned.
source_table
Supplementary table from which the row was derived.
Quality control
The authors used separate converted-reference alignment paths for C→T and G→A reads, ignored bases not matching the expected wild-type or converted identities, and applied Benjamini-Hochberg correction to position-level G tests. Significant wild-type depletion was defined using the reported Z-score and adjusted-p-value rules. Package QC retained all 1,941 Supplementary Data 4 rows with complete identifiers, finite effect/statistical fields, and P_adj <= 0.05; the source table is already a significance-filtered result table. No raw read reanalysis was performed.
Curation notes
The processed table is a nucleotide-level mutational readout, not a list of ordinary genetic variants: converted_base represents the experimentally induced C→T or G→A state. The paper text reports 2,060 significant positions, while the deposited Supplementary Data 4 file contains 1,941 rows; this package uses the deposited table without inventing the missing entries. Blank overlapping_region cells correspond to the source table's '.' placeholder.