An RNA-element selection assay (RESA) was performed by injecting an in-vitro-transcribed, high-density reporter library containing endogenous 3′-UTR fragments into one-cell-stage wild-type zebrafish embryos. This package represents the public WT total-RNA targeted-library profile as overlapping sequence windows with the 2-to-6 hpf stability score used as input to the authors' random-forest model.
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
Basal / Untreated
RESA used an SP6-promoter/GFP reporter with endogenous transcript fragments in the 3′ UTR and an SV40 polyadenylation signal. The in-vitro-transcribed RNA library was injected into one-cell embryos; reporter fragments were quantified by RNA-seq at developmental stages including 2 and 6 hpf. The authors normalized positional coverage to counts per million, and the model input used 100-nt sliding windows at a 10-nt step. The packaged WindowRESA value is the WT total-RNA stability score for each source window, in log2 6 hpf/2 hpf units.
Processed data
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Visible columns (13 of 13)
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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 · 13 definitions
element_id
Unique identifier assigned to the packaged RESA window in source-file order.
source_row
One-based row number in the authors' WindowSequences.csv source, including its header as row 1.
source_wind_id
Original composite identifier combining Ensembl transcript ID, Ensembl gene ID, and source gene label.
transcript_id
Ensembl transcript identifier parsed from source_wind_id (Ensembl release 78 context).
gene_id
Ensembl zebrafish gene identifier parsed from source_wind_id.
gene_symbol
Gene symbol or source label parsed from source_wind_id; source disambiguation text is retained when present.
window_index
One-based ordinal of the window within the source transcript profile.
window_start_0based
Nominal zero-based start inferred from the published 10-nt sliding-window step and window_index.
window_end_0based_exclusive
Nominal start plus the actual length of the source sequence; the source contains a small number of sequences longer than 100 nt, which are preserved.
utr_length_nt
Source 3′-UTR length in nucleotides.
sequence
Source nucleotide sequence for the RESA window, represented with the DNA alphabet used by the distributed file.
sequence_length_nt
Length of sequence in nucleotides.
resa_stability_log2_6h_over_2h
Authors' WindowRESA stability score for the WT total-RNA targeted RESA profile, representing log2 reporter abundance at 6 hpf relative to 2 hpf and used for random-forest model training.
Quality control
The source WindowSequences.csv had already undergone the authors' RESA positional-coverage/CPM processing. Package QC retained a row only when the score was finite and numeric, the composite identifier and positive UTR length were present, the sequence contained only A/C/G/T/N and was at least 100 nt, and the inferred window end (10-nt step from the within-transcript row order) did not exceed the source UTR length. All 25,044 source rows passed these checks; no rows were excluded. The source table has no per-replicate counts or barcode-level coverage, so replicate-level coverage thresholds could not be independently reapplied.
Curation notes
This is a public processed model input rather than a newly re-counted barcode matrix. The study also generated a ∼30-nt transcriptome library and additional WT, α-amanitin, LNA-430, and poly(A)-selected RESA conditions; their sequencing runs are documented in raw_data/SRP189389_SRA_runinfo.csv and the paper also cites the earlier SRP090954 submission, but raw SRA reads were intentionally not downloaded. The packaged model input contains 291 source transcript profiles and 25,044 windows. Nominal window coordinates are an inference from the paper's 10-nt sliding-window description; the original sequence lengths and scores are preserved verbatim.