CircLibA and NucLibA sequence tiles were cloned into WT beta-globin (spliced), beta-globin-Delta introns (unspliced), circPVT1, and scrambled circPVT1 reporter backbones and transfected into MCF-7 cells. Nuclear, cytoplasmic, whole-cell, and plasmid-input measurements were used to report context-specific localization and expression effects.
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
Basal / Untreated
MCF-7 cells were transfected with plasmid pools containing 110-nt NucLibA or 140-nt CircLibA tiles in four RNA contexts. After 24 h, nuclear and cytoplasmic fractions plus whole-cell extract were collected; tile amplicons were counted from 150-nt single-end reads using a UMI and adapter-aware matching procedure. The source ratios are normalized log2 Nuc/Cyto and WCE/plasmid-input measurements with a 0.5 pseudocount, as described by the authors.
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 · 25 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_nuc_cyto_log2
Author-reported log2 nuclear/cytoplasmic localization ratio in the WT beta-globin spliced context.
unspliced_nuc_cyto_log2
Author-reported log2 nuclear/cytoplasmic localization ratio in the beta-globin-Delta introns unspliced context.
circpvt1_nuc_cyto_log2
Author-reported log2 nuclear/cytoplasmic localization ratio in the circPVT1 circular context.
scrcircpvt1_nuc_cyto_log2
Author-reported log2 nuclear/cytoplasmic localization ratio in the scrambled-circPVT1 circular context.
spliced_expression_log2_wce_plasmid
Author-reported log2 whole-cell-extract/plasmid-input expression ratio in the spliced context.
unspliced_expression_log2_wce_plasmid
Author-reported log2 whole-cell-extract/plasmid-input expression ratio in the unspliced context.
circpvt1_expression_log2_wce_plasmid
Author-reported log2 whole-cell-extract/plasmid-input expression ratio in the circPVT1 context.
scrcircpvt1_expression_log2_wce_plasmid
Author-reported log2 whole-cell-extract/plasmid-input expression ratio in the scrambled-circPVT1 context.
spliced_nuc_cyto_pvalue
Author-reported P-value accompanying the spliced-context localization result.
unspliced_nuc_cyto_pvalue
Author-reported P-value accompanying the unspliced-context localization result.
circpvt1_nuc_cyto_pvalue
Author-reported P-value accompanying the circPVT1 localization result.
scrcircpvt1_nuc_cyto_pvalue
Author-reported P-value accompanying the scrambled-circPVT1 localization result.
spliced_expression_pvalue
Author-reported P-value accompanying the spliced-context expression result.
unspliced_expression_pvalue
Author-reported P-value accompanying the unspliced-context expression result.
circpvt1_expression_pvalue
Author-reported P-value accompanying the circPVT1 expression result.
scrcircpvt1_expression_pvalue
Author-reported P-value accompanying the scrambled-circPVT1 expression result.
Quality control
The authors retained only fragments with at least 20 mapped reads after requiring the expected adapter, extracting the UMI, and matching reads to library sequences with their stated quality and mismatch limits; ambiguous equal-best matches were discarded. For this package, rows were additionally required to have an official nucLib or circLib label, a nonempty tested sequence, and at least one source localization or expression result. This retained 7,979 rows from 8,162 source rows and excluded the five unlabeled/non-assay rows plus 178 labeled library rows with no core result. No additional biological effect-size threshold was applied.
Curation notes
This table is a cleaned projection of Supplementary Data 3 finalTab_230221; it contains source-derived ratios rather than reconstructed barcode counts. Missing values mean that the tile was not quantified in that specific context after the authors' read filter. The paper also reports a sequence-matched linear-circPVT1 comparison, but its numeric results are not present in the supplied finalTab and were not inferred here. The sequence library includes human and orthologous noncoding-RNA tiles, so no single reference genome is assigned.