A RESA reporter RNA library was co-injected with FLAG-tagged Ago2 into zebrafish embryos, UV-crosslinked, and immunoprecipitated with anti-FLAG beads. Ago2-bound reporter fragments were compared with the input library to identify RNA regions enriched for Ago2/miR-430-associated binding.
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
Co-injection of 80 pg FLAG-tagged Ago2 with 80 pg RESA library; 254 nm UV crosslinking at approximately 3.3 hpf followed by anti-FLAG immunoprecipitation
The RESA-CLIP assay used 800 zebrafish embryos, 80 pg RESA library and 80 pg FLAG-tagged Ago2, 254 nm UV crosslinking for 4 minutes on ice at 30% epiboly, FLAG M2 magnetic-bead immunoprecipitation, and sequencing of input and IP RNA. The source analysis limited each UTR position to two read-fragment starts or ends, except at UTR boundaries, to reduce PCR artifacts.
RESA-CLIP RNA reporter assay: a common GFP-3′UTR reporter RNA library was co-injected with FLAG-Ago2, UV-crosslinked in vivo, immunoprecipitated with anti-FLAG magnetic beads, and sequenced. The readout is Ago2 IP-versus-input fragment enrichment rather than a conventional RNA-stability or transcriptional activity score.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (11 of 11)
Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
Page 1 · 50 rows · More results available
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 11 definitions
clip_peak_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 5.
gene_symbol
Gene symbol suffix parsed from the source UTR identifier.
coordinate_zv9
Broad genomic interval of the Ago2-enriched peak on zebrafish Zv9.
critical_point_utr
UTR-relative position used to center the CLIP peak.
log2_clip_vs_input
Published log2 Ago2 CLIP-versus-input enrichment.
clip_vs_input_fold_enrichment
Derived CLIP/input fold enrichment, calculated as 2 raised to log2_clip_vs_input.
width_nt
Width of the Ago2-enriched peak in nucleotides.
clip_coverage
Published CLIP coverage at the peak.
resa_destabilized_class
Published overlap class indicating whether the peak overlaps a RESA destabilized region, including MIR430, NON-MIR430, LOW-CONFIDENCE, BOTH_ADJACENT, or blank.
source_table
Supplementary table from which the row was derived.
Quality control
The authors mapped CLIP and input reads using the RESA alignment strategy and limited overlapping read-fragment starts or ends to two per UTR position to reduce PCR artifacts. Package QC retained all 135 Supplementary Data 5 peak rows with nonmissing coordinates, finite log2 enrichment, positive width, and CLIP coverage >= 50X. No raw read reanalysis was performed.
Curation notes
The two relevant SRA runs are SRR4375299 (RESA-CLIP Ago2 IP) and SRR4375300 (RESA-CLIP Ago2 input). The source table's RESA_Destabilized? field is an overlap annotation, not a second CLIP significance measure; blank values correspond to '.'.