The same sequence-tile reporters were transfected into MCF-7 cells and transcription was inhibited with actinomycin D. Expression was measured at 2, 4, and 8 h, normalized to spiked Renilla luciferase controls, and used to estimate tile half-lives in spliced, unspliced, and circular reporter contexts.
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:0031
Reference genome
Not reported / not applicable
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
5 microgram/ml actinomycin D for 2, 4, or 8 h; DMSO control
Twenty-four hours after plasmid transfection, cells received actinomycin D or DMSO and were harvested at 2, 4, and 8 h. Two in-vitro-transcribed Renilla luciferase RNA oligos were spiked into the extraction and used for normalization. The authors fitted a linear regression of expression over time and calculated half-life from the fitted intercept and slope; the table retains the author-reported fit statistic and half-life estimates for three host-RNA contexts.
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.
Column dictionary · 15 definitions
element_id
Unique tested tile identifier from the source finalTab row name.
library
Source library label: nucLib for NucLibA or circLib for CircLibA.
library_index
Numeric tile index supplied by the source table.
segment_name
Author-provided segment name for the tested tile.
gene_name
Source gene or noncoding-RNA name from which the tile was derived.
sequence
Nucleotide sequence of the tested tile.
sequence_length
Length of the tested sequence in nucleotides, calculated from sequence.
gc_percent
GC content of the tile in percent, as supplied by the authors.
delta_g_kcal_mol
RNAfold-predicted minimum free energy (DeltaG) in kcal/mol, as supplied by the authors.
spliced_fit_r
Author-reported R fit statistic for the spliced-context stability regression.
circular_fit_r
Author-reported R fit statistic for the circular-context stability regression.
unspliced_fit_r
Author-reported R fit statistic for the unspliced-context stability regression.
spliced_half_life_h
Author-estimated spliced-context tile half-life in hours.
circular_half_life_h
Author-estimated circular-context tile half-life in hours.
unspliced_half_life_h
Author-estimated unspliced-context tile half-life in hours.
Quality control
The authors used the same adapter/UMI-aware read matching and minimum 20-read fragment filter described for the main MPRNA, normalized expression to luciferase spike-ins, and calculated half-lives from linear fits over the 2, 4, and 8 h time points. For this package, rows were required to have an official nucLib or circLib label, a nonempty sequence, and at least one source stability fit statistic or half-life estimate. This retained 7,112 rows from 8,162 source rows; the five unlabeled/non-assay rows and library rows without stability output were excluded. Negative or extreme fitted half-life estimates were retained when supplied by the authors rather than removed by an arbitrary biological cutoff.
Curation notes
This table is a cleaned projection of the stability columns in Supplementary Data 3 finalTab_230221. It reports author-derived regression outputs, not raw time-point counts. The source values include some negative or very large fitted half-lives, which can arise from extrapolation of a short linear time course; these were preserved and are explicitly noted rather than silently censored. The authors state that the stability follow-up used circPVT1 rather than SCRcircPVT1 circular vectors.