Transient episomal minigene reporter libraries tested randomized or degenerate sequence contexts from human 3′ UTRs in HEK293T cells. RNA-seq-derived UMI counts quantify proximal, distal/non-proximal, and de novo cleavage outcomes for millions of reporters.
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
GRCh37
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
The construct is an episomal 3′ UTR APA minigene reporter. The GEO isoform export reports unique UMI counts in proximal and distal/non-proximal cleavage regions plus average and standard deviation of proximal cleavage position; seq is 186 nt with the proximal PAS at position 50, and seq_ext is a 256-nt padded representation retained only in raw_data.
Processed data
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Visible columns (11 of 11)
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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 · 11 definitions
reporter_id
Stable sequential identifier assigned to a retained processed reporter.
sequence
The 186-nt reporter sequence from GEO; X denotes a source-provided masked/flanking position.
library_id
GEO/APARENT numeric library identifier.
library_name
GEO/APARENT library name.
proximal_count
Unique UMI count assigned to the proximal cleavage region.
total_count_vs_distal
Unique UMI count assigned to proximal or distal cleavage regions, used as the proximal-fraction denominator.
total_count_vs_all
Unique UMI count assigned anywhere on the reporter, including de novo cleavage sites.
proximal_fraction_vs_distal
Derived proximal_count / total_count_vs_distal.
proximal_fraction_vs_all
Derived proximal_count / total_count_vs_all.
proximal_avgcut
Source-reported mean cleavage position within the proximal region; empty when undefined.
proximal_stdcut
Source-reported standard deviation of cleavage position within the proximal region; empty when undefined.
Quality control
Starting from GEO GSE113849_data_isoforms.csv.gz, retained the APARENT processing-code random/degenerate library IDs 2, 5, 8, 11, 20, 22, and 30–35. Retained rows required a 186-nt source sequence containing only A/C/G/T/N/X, integer count fields, total_count_vs_all ≥ 20, and total_count_vs_distal > 0; rows failing these available-data checks were excluded. proximal_avgcut and proximal_stdcut are left empty when the source has no proximal-cleavage UMI, rather than discarding otherwise adequately covered reporters.
Curation notes
This table contains 2,039,869 retained reporters across the selected random/degenerate libraries. The GEO compact export is sequence-level and does not expose biological replicate columns. Library 20 (DoubleDope) contains X mask characters in the source sequence and was retained because these symbols are part of the deposited sequence representation. The source processing code used a minimum total-count threshold of 1 for the random dataset; the stricter 20-count export filter was applied here for a cleaner table. The article text abbreviates the cell line as HEK293 and its resource table lists HEK293FT, while the GEO sample records explicitly identify HEK293T; the biosample mapping follows GEO (CVCL:0063). The article also performed a separate designed/native PAS MPRA; this package includes its measured variant summary as the second experiment because the compact GEO file does not expose a separable designed-library table.