SH-SY5Y full PTRE-seq 3′ UTR reporter library
U-rich elements drive pervasive cryptic splicing in 3’ UTR massively parallel reporter assaysThree biological SH-SY5Y RNA replicates of the 642-reporter synthetic PTRE-seq library, with ten internal barcode copies per reporter identity. Extended reporter amplicon sequencing quantified full-length and cryptically spliced transcript classes.
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.
Perturbation & assay details
Basal / Untreated
Episomal GFP PTRE-seq 3′-UTR reporter library. Extended amplicons spanning the GFP coding sequence and most of the 3′ UTR were used to classify full-length and cryptically spliced transcripts; the RNA readout was summarized across internal barcodes and replicates.
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 · 33 definitions
- reporter_id
- Canonical PTRE-seq reporter identity; synthetic module arrays use four module codes and named controls retain their published names.
- reporter_class
- Library design class: synthetic module array, natural let-7 control, or low-expression control.
- module_1
- Synthetic 3′ UTR module at position 1 (B=blank, A=AU-rich element, L=let-7 site, p=Pumilio site, S=Smaug site); blank for named controls.
- module_2
- Synthetic 3′ UTR module at position 2; blank for named controls.
- module_3
- Synthetic 3′ UTR module at position 3; blank for named controls.
- module_4
- Synthetic 3′ UTR module at position 4; blank for named controls.
- are_count
- Number of AU-rich element (A) modules in the synthetic reporter identity.
- let7_site_count
- Number of let-7 site (L) modules in the synthetic reporter identity.
- pumilio_site_count
- Number of Pumilio site (p) modules in the synthetic reporter identity.
- smaug_site_count
- Number of Smaug site (S) modules in the synthetic reporter identity.
- blank_count
- Number of blank (B) modules in the synthetic reporter identity.
- library_barcode_count
- Number of internal barcode copies assigned to the reporter in barcode_indexed.txt.
- full_length_fraction
- Released median fraction (0–1) of classified RNA reads assigned to the full-length reporter.
- spliced_fraction
- Complement of full_length_fraction (1 − full_length_fraction), representing classified RNA reads assigned to cryptic splice isoforms.
- dominant_splice_event
- Most abundant released cryptic-splicing category for the reporter; category encodes donor sequence, donor position, acceptor sequence, and acceptor position.
- dominant_splice_event_fraction
- Released fraction (0–1) for the dominant cryptic-splicing category.
- detected_splice_event_count
- Number of non-full-length splice categories reported for the reporter in the released quantification.
- barcode_measurement_count
- Number of reporter-copy/sample measurements passing the >10 classified-read filter in the raw count files.
- full_length_barcode_measurement_count
- Passing reporter-copy/sample measurements with at least one full-length read.
- spliced_barcode_measurement_count
- Passing reporter-copy/sample measurements with at least one classified spliced read.
- full_length_read_count
- Sum of full-length classified read counts across passing reporter-copy/sample measurements.
- spliced_read_count
- Sum of classified spliced read counts across passing reporter-copy/sample measurements.
- classified_read_count
- Sum of full-length and classified spliced reads across passing reporter-copy/sample measurements.
- dna_full_length_fraction
- Released median full-length fraction from the two DNA plasmid input libraries.
- dna_spliced_fraction
- Complement of dna_full_length_fraction.
- dna_classified_read_count
- Full-length plus classified spliced DNA-input reads across passing DNA reporter-copy measurements.
- spliceai_predicted_probability
- Median product of the best donor and best acceptor SpliceAI probabilities across reporter copies.
- spliceai_best_donor_position
- Modal best donor position in the reconstructed PTRE-seq transcript used for SpliceAI prediction.
- spliceai_best_acceptor_position
- Modal best acceptor position in the reconstructed PTRE-seq transcript used for SpliceAI prediction.
- spliceai_donor_probability
- Median SpliceAI probability for the best donor across reporter copies.
- spliceai_acceptor_probability
- Median SpliceAI probability for the best acceptor across reporter copies.
- spliceai_prediction_copies
- Number of reporter copies with a released SpliceAI prediction.
- qc_pass
- TRUE when the reporter has a released full-length summary and passes the reporter-level barcode/read QC threshold.
Quality control
Authors' released pipeline classified extended-amplicon reads as full_length or spliced after barcode demultiplexing and removed other categories. For each barcode/sample measurement, classified full_length + spliced counts had to exceed 10 reads; reporter identities required more than 5 passing full-length barcode measurements. The raw files independently retain 642 QC-passing reporter identities across 18047 passing barcode/sample measurements. The table uses the authors' released reporter-level fraction/event file for the primary fractions and event labels, and raw count files for independently summarized read/QC columns.
Curation notes
SH-SY5Y basal cell condition; no treatment or trans-factor perturbation was reported for this packaged run. The library contains 625 combinations of four modules (B/A/L/p/S) plus 17 named controls, with internal barcode copies represented in the barcode map. The inserts are synthetic; GRCh38 is recorded only because the paper uses it for comparison to annotated human splice sites and SpliceAI, not because reporter rows are genomic coordinates. The released fraction file is treated as authoritative for reporter-level splicing fractions; raw category counts remain available under raw_data for audit and reprocessing.