Experiment / E4SOLQBSNEpisomal Plasmid MPRA

PolyU+/− random intron validation MPRA

Sequence-dependent and -independent effects of intron-mediated enhancement learned from thousands of random introns

A smaller validation library tested 30 parent random introns in original, U4-deleted, and U4-added sequence forms, for 90 designed intron sequences, together with intronless controls. The pool was transiently transfected into HEK293T A2 cells and assayed by two-replicate RNA-seq of dTomato, spliced GFP, and unspliced GFP reporter reads.

Download processed table (CSV)Raw source data API documentation

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:0063
Reference genome: Not reported / not applicable
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Transient transfection; polyU/U4 deletion or addition variants

This validation library was the exception to the study’s integrated reporter experiments: the pool was transiently transfected, and RNA was collected for two replicate reporter-count measurements. Each oligo uses a dual dTomato/GFP reporter with a barcode; the 30 parent introns were minimally permuted to disperse or cluster U residues, producing the original, polyU4-deleted, and polyU4-added conditions. polyU counts in this package count overlapping TTT/TTTT/TTTTT motifs in the variable intron region.

Processed data

50 rows per page. Click a cell to inspect its full value.

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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 · 31 definitions

element_id: Stable package identifier for the oligo-level validation element.
oligo_id: Source oligo identifier from the GEO workbook.
description: Source library description identifying the parent intron or intronless control.
barcode: Reporter barcode associated with the oligo.
parent_intron: Normalized parent random-intron identifier for variants; blank for intronless controls.
condition: Normalized design condition: original, polyU4_deleted, polyU4_added, or intronless_control.
intron_sequence: Full deposited intron sequence; blank for intronless controls.
random_region_sequence: Internal variable sequence after removing the constant splice-site flanks; blank for controls.
intron_length: Length of the full deposited intron sequence in nucleotides; blank for controls.
random_region_length: Length of the variable internal sequence in nucleotides; blank for controls.
polyU3_count: Number of overlapping TTT motifs in the variable region.
polyU4_count: Number of overlapping TTTT motifs in the variable region.
polyU5_count: Number of overlapping TTTTT motifs in the variable region.
random_region_gc_fraction: Fraction of variable-region bases that are G or C.
count_completeness: Whether both replicate spliced-GFP source cells were populated (complete) or at least one was blank (missing_spliced_GFP).
dtom_rep1: Deposited dTomato read count for replicate 1.
gfp_spliced_rep1: Deposited spliced-GFP read count for replicate 1; blank source cells are preserved as blank.
gfp_unspliced_rep1: Deposited unspliced-GFP read count for replicate 1.
gfp_total_rep1: Spliced plus unspliced GFP count for replicate 1; a blank source spliced-GFP cell contributes zero only to this derived total.
total_reads_rep1: dTomato plus total GFP classified reads for replicate 1.
raw_log2_gfp_dtom_ratio_rep1: Non-normalized log2((1 + total GFP) / (1 + dTomato)) for replicate 1; blank when spliced-GFP data are incomplete.
splicing_efficiency_rep1: Spliced-GFP divided by total GFP for replicate 1; blank when spliced-GFP data are incomplete or total GFP is zero.
dtom_rep2: Deposited dTomato read count for replicate 2.
gfp_spliced_rep2: Deposited spliced-GFP read count for replicate 2; blank source cells are preserved as blank.
gfp_unspliced_rep2: Deposited unspliced-GFP read count for replicate 2.
gfp_total_rep2: Spliced plus unspliced GFP count for replicate 2; a blank source spliced-GFP cell contributes zero only to this derived total.
total_reads_rep2: dTomato plus total GFP classified reads for replicate 2.
raw_log2_gfp_dtom_ratio_rep2: Non-normalized log2((1 + total GFP) / (1 + dTomato)) for replicate 2; blank when spliced-GFP data are incomplete.
splicing_efficiency_rep2: Spliced-GFP divided by total GFP for replicate 2; blank when spliced-GFP data are incomplete or total GFP is zero.
mean_raw_log2_gfp_dtom_ratio: Mean of the two replicate raw ratios; blank when either replicate has incomplete spliced-GFP data.
min_total_reads_across_replicates: Smaller of the two replicate total classified-read counts.

Quality control

Applied the study's stated polyU-library filter of at least 100 total classified reads per replicate, where total is dTomato + spliced GFP + unspliced GFP. This retained 278 of 280 source rows and excluded 2 low-count rows (o_42408, o_42806). Source-cell blanks for spliced GFP are preserved and are not imputed.

Curation notes

The direct GEO workbook contains 280 rows: 90 original parent introns, 90 U4-deleted designs, 90 U4-added designs, and 10 intronless controls. For U4-added/deleted rows, the deposited spliced-GFP cells are blank while low unspliced-GFP counts are present; this package preserves those blanks and does not substitute unavailable values. The public supplementary S9 sheet has one fewer row than the direct GEO workbook, so the direct GEO workbook is the source for this table.

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