C3U Flp-In-293 pooled 3′-UTR activity screen
Systematic identification of regulatory elements in conserved 3′-untranslated regions of human transcriptsTwo independently generated C3U libraries of 16,332 conserved human 34-nt 3′-UTR elements were tested in pooled Flp-In-293 cells. FACS expression bins and high-throughput sequencing of reporter-insert amplicons were used to identify elements enriched in high- or low-DIR populations.
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
A bidirectional CMV-GFP/mCherry reporter carrying each insert in the mCherry 3′ UTR was recombinase-integrated at the single FRT locus of Flp-In-293 cells. GFP-positive cells were sorted into approximately 10% DIR bins (H10, H20, H30, H40, L10, L20, L30, L40), and genomic-DNA amplicons were sequenced; GEO supplies technical-replicate-consolidated and adjacent-bin-merged counts and log2 frequencies for independent library constructions A and B.
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 · 42 definitions
- element_id
- Unique C3U library sequence identifier.
- sequence
- The tested 34-nt conserved 3′-UTR sequence.
- sequence_length
- Length of the tested sequence in nucleotides.
- published_prediction_id
- Publisher Table S2 ranked prediction identifier, such as C3U-R1 or C3U-A1; blank when not in Table S2.
- published_activity_call
- Publisher Table S2 call: repressor or activator.
- published_prediction_rank
- Numeric rank parsed from the publisher prediction identifier.
- published_log_high_vs_low
- Publisher Table S2 log2(high-DIR frequency/low-DIR frequency) value.
- published_q_value
- Publisher Table S2 Benjamini-Hochberg q-value.
- library_a_background_count
- Library A background-population count supplied by GEO.
- library_b_background_count
- Library B background-population count supplied by GEO.
- library_a_h10_h20_count
- Library A raw read count in the merged H10/H20 high-DIR bins.
- library_a_h10_h20_log2_relative_freq
- Library A GEO-supplied log2 normalized frequency relative to background in H10/H20.
- library_a_h30_h40_count
- Library A raw read count in the merged H30/H40 high-DIR bins.
- library_a_h30_h40_log2_relative_freq
- Library A GEO-supplied log2 normalized frequency relative to background in H30/H40.
- library_a_l10_l20_count
- Library A raw read count in the merged L10/L20 low-DIR bins.
- library_a_l10_l20_log2_relative_freq
- Library A GEO-supplied log2 normalized frequency relative to background in L10/L20.
- library_a_l30_l40_count
- Library A raw read count in the merged L30/L40 low-DIR bins.
- library_a_l30_l40_log2_relative_freq
- Library A GEO-supplied log2 normalized frequency relative to background in L30/L40.
- library_b_h10_h20_count
- Library B raw read count in the merged H10/H20 high-DIR bins.
- library_b_h10_h20_log2_relative_freq
- Library B GEO-supplied log2 normalized frequency relative to background in H10/H20.
- library_b_h30_h40_count
- Library B raw read count in the merged H30/H40 high-DIR bins.
- library_b_h30_h40_log2_relative_freq
- Library B GEO-supplied log2 normalized frequency relative to background in H30/H40.
- library_b_l10_l20_count
- Library B raw read count in the merged L10/L20 low-DIR bins.
- library_b_l10_l20_log2_relative_freq
- Library B GEO-supplied log2 normalized frequency relative to background in L10/L20.
- library_b_l30_l40_count
- Library B raw read count in the merged L30/L40 low-DIR bins.
- library_b_l30_l40_log2_relative_freq
- Library B GEO-supplied log2 normalized frequency relative to background in L30/L40.
- library_a_high_mean_log2_relative_freq
- Mean Library A log2 relative frequency across high-DIR bins with >20 reads.
- library_a_low_mean_log2_relative_freq
- Mean Library A log2 relative frequency across low-DIR bins with >20 reads.
- library_a_high_vs_low_log2_effect
- Library A high-DIR mean minus low-DIR mean; positive indicates high-DIR enrichment.
- library_b_high_mean_log2_relative_freq
- Mean Library B log2 relative frequency across high-DIR bins with >20 reads.
- library_b_low_mean_log2_relative_freq
- Mean Library B log2 relative frequency across low-DIR bins with >20 reads.
- library_b_high_vs_low_log2_effect
- Library B high-DIR mean minus low-DIR mean; positive indicates high-DIR enrichment.
- combined_high_mean_log2_relative_freq
- Mean of all available high-DIR log2 relative frequencies from bins with >20 reads.
- combined_low_mean_log2_relative_freq
- Mean of all available low-DIR log2 relative frequencies from bins with >20 reads.
- combined_high_vs_low_log2_effect
- Combined high-DIR mean minus low-DIR mean; positive indicates high-DIR enrichment and negative indicates low-DIR enrichment.
- replicate_effect_difference
- Library A high-vs-low effect minus Library B high-vs-low effect when both library-specific effects are estimable.
- n_high_bins_gt20
- Number of high-DIR merged-bin files with more than 20 reads across libraries A and B.
- n_low_bins_gt20
- Number of low-DIR merged-bin files with more than 20 reads across libraries A and B.
- n_library_replicates_with_both_sides
- Number of library constructions for which both a high-DIR and a low-DIR bin exceeded 20 reads.
- effect_direction
- Direction from the combined derived effect: high_DIR_enriched, low_DIR_enriched, or neutral.
- published_direction_concordance
- Whether the derived effect direction agrees with the publisher's repressor/activator call.
- qc_pass
- TRUE for rows retained after the package QC filter.
Quality control
The authors retained reads containing both terminal universal adapters, matched reads to the synthetic C3U library, consolidated technical replicates, merged adjacent bins, normalized each sorted-bin frequency to its library background population, required more than 20 counts in a sample for downstream sequence analysis, and excluded sequences seen only in background. They called repressors or activators with a high-versus-low DIR frequency difference of at least twofold and Benjamini-Hochberg q-value <0.05. For this package, a row was retained only if its sequence was 34 nt of A/C/G/T, had nonzero background representation in at least one library, and had >20 reads in at least one high-DIR and one low-DIR merged-bin file across the two libraries; summary effects use only bins passing the >20-count threshold. This retained 5,668 of the 12,970 sequence IDs present in the GEO processed files.
Curation notes
The paper presents a custom pooled post-transcriptional reporter screen rather than using the MPRA acronym, but it meets the MPRA definition operationally: thousands of regulatory inserts are assayed in parallel by a reporter, sorted by expression, and quantified by sequencing. The primary classification is Sort-Seq / Flow-Seq MPRA because FACS binning is the assay readout; the single-locus Flp recombinase integration is documented in assay_type_additional_details. Libraries A and B are independent library constructions under the same HEK293 condition and are packaged as one experiment. GEO's published log2 relative frequencies are preserved for every bin, while derived means ignore bins with <=20 reads. The combined effect can be estimable even when no individual library has both sides covered; those cases are marked by n_library_replicates_with_both_sides and have blank library-specific effect differences where appropriate. Table S2 annotations are joined by element_id when available.