HeLa PTRE-seq multi-fraction synthetic 3′UTR library
PTRE-seq reveals mechanism and interactions of RNA binding proteins and miRNAsAn episomal CMV/TO-EGFP reporter library containing 642 synthetic 3′UTR identities, each represented by barcoded oligonucleotides, was transfected into HeLa cells. Total RNA, polysome-associated RNA, and 40S-associated RNA were quantified against plasmid input to measure RNA expression, translation efficiency, translation initiation, and 40S association.
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
Standard episomal plasmid MPRA configuration: synthetic 3′UTR elements were cloned downstream of a CMV/TO-driven EGFP reporter and each insert was linked to a co-transcribed 9-bp barcode. HeLa cells were harvested 40 h after electroporation; total RNA and cycloheximide-stabilized 40S/polysome fractions were barcode-sequenced. The source analysis normalized barcode counts to the mean of two plasmid-input replicates and to the median 4×Blank control.
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 · 51 definitions
- construct_id
- Canonical synthetic 3′UTR reporter identity from the source library.
- construct_class
- Curated class of the reporter identity: blank control, synthetic element combination, let-7 variant, natural let-7 target, or let-7 copy-number variant.
- element_position_1
- Regulatory element at synthetic 3′UTR position 1; blank for special variant/natural-target identities whose positional encoding is not explicit in the identity label.
- element_position_2
- Regulatory element at synthetic 3′UTR position 2; blank for special variant/natural-target identities whose positional encoding is not explicit in the identity label.
- element_position_3
- Regulatory element at synthetic 3′UTR position 3; blank for special variant/natural-target identities whose positional encoding is not explicit in the identity label.
- element_position_4
- Regulatory element at synthetic 3′UTR position 4; blank for special variant/natural-target identities whose positional encoding is not explicit in the identity label.
- regulatory_sequence
- 132-nt synthetic regulatory-element sequence from Supplementary Data 1, with source capitalization retained.
- regulatory_sequence_length_nt
- Length of the source regulatory-element sequence in nucleotides.
- library_barcode_count
- Number of distinct source barcodes assigned to this reporter identity.
- qc_barcode_count
- Number of barcodes retained after the package read-count QC filter.
- plasmid_count_rep1_mean
- Mean raw plasmid-input read count per QC-passing barcode in plasmid replicate 1.
- plasmid_count_rep2_mean
- Mean raw plasmid-input read count per QC-passing barcode in plasmid replicate 2.
- rna_count_rep1_mean
- Mean raw total-RNA read count per QC-passing barcode in replicate 1.
- rna_count_rep2_mean
- Mean raw total-RNA read count per QC-passing barcode in replicate 2.
- rna_count_rep3_mean
- Mean raw total-RNA read count per QC-passing barcode in replicate 3.
- rna_count_rep4_mean
- Mean raw total-RNA read count per QC-passing barcode in replicate 4.
- polysome_count_rep1_mean
- Mean raw polysome-associated RNA read count per QC-passing barcode in replicate 1.
- polysome_count_rep2_mean
- Mean raw polysome-associated RNA read count per QC-passing barcode in replicate 2.
- polysome_count_rep3_mean
- Mean raw polysome-associated RNA read count per QC-passing barcode in replicate 3.
- polysome_count_rep4_mean
- Mean raw polysome-associated RNA read count per QC-passing barcode in replicate 4.
- forty_s_count_rep1_mean
- Mean raw 40S-associated RNA read count per QC-passing barcode in replicate 1.
- forty_s_count_rep2_mean
- Mean raw 40S-associated RNA read count per QC-passing barcode in replicate 2.
- rna_expression_log2_rep1
- Median barcode-level log2 total-RNA expression relative to the 4×blank (BBBB) control in replicate 1.
- rna_expression_log2_rep2
- Median barcode-level log2 total-RNA expression relative to the 4×blank (BBBB) control in replicate 2.
- rna_expression_log2_rep3
- Median barcode-level log2 total-RNA expression relative to the 4×blank (BBBB) control in replicate 3.
- rna_expression_log2_rep4
- Median barcode-level log2 total-RNA expression relative to the 4×blank (BBBB) control in replicate 4.
- rna_expression_log2_median
- Median of all QC-passing barcode-level log2 total-RNA expression values across the available replicates.
- rna_expression_log2_mean
- Arithmetic mean of all QC-passing barcode-level log2 total-RNA expression values across the available replicates.
- rna_expression_log2_sd
- Sample standard deviation of all QC-passing barcode-level log2 total-RNA expression values across the available replicates.
- rna_expression_log2_observations
- Number of barcode-by-replicate observations contributing to the total-RNA expression summary.
- translation_efficiency_log2_rep1
- Median barcode-level log2 translation efficiency relative to the 4×blank (BBBB) control in replicate 1.
- translation_efficiency_log2_rep2
- Median barcode-level log2 translation efficiency relative to the 4×blank (BBBB) control in replicate 2.
- translation_efficiency_log2_rep3
- Median barcode-level log2 translation efficiency relative to the 4×blank (BBBB) control in replicate 3.
- translation_efficiency_log2_rep4
- Median barcode-level log2 translation efficiency relative to the 4×blank (BBBB) control in replicate 4.
- translation_efficiency_log2_median
- Median of all QC-passing barcode-level log2 translation efficiency values across the available replicates.
- translation_efficiency_log2_mean
- Arithmetic mean of all QC-passing barcode-level log2 translation efficiency values across the available replicates.
- translation_efficiency_log2_sd
- Sample standard deviation of all QC-passing barcode-level log2 translation efficiency values across the available replicates.
- translation_efficiency_log2_observations
- Number of barcode-by-replicate observations contributing to the translation efficiency summary.
- forty_s_association_log2_rep1
- Median barcode-level log2 40S association relative to the 4×blank (BBBB) control in replicate 1.
- forty_s_association_log2_rep2
- Median barcode-level log2 40S association relative to the 4×blank (BBBB) control in replicate 2.
- forty_s_association_log2_median
- Median of all QC-passing barcode-level log2 40S association values across the available replicates.
- forty_s_association_log2_mean
- Arithmetic mean of all QC-passing barcode-level log2 40S association values across the available replicates.
- forty_s_association_log2_sd
- Sample standard deviation of all QC-passing barcode-level log2 40S association values across the available replicates.
- forty_s_association_log2_observations
- Number of barcode-by-replicate observations contributing to the 40S association summary.
- translation_initiation_efficiency_log2_rep1
- Median barcode-level log2 translation initiation efficiency (polysome/40S) relative to the 4×blank (BBBB) control in replicate 1.
- translation_initiation_efficiency_log2_rep2
- Median barcode-level log2 translation initiation efficiency (polysome/40S) relative to the 4×blank (BBBB) control in replicate 2.
- translation_initiation_efficiency_log2_median
- Median of all QC-passing barcode-level log2 translation initiation efficiency (polysome/40S) values across the available replicates.
- translation_initiation_efficiency_log2_mean
- Arithmetic mean of all QC-passing barcode-level log2 translation initiation efficiency (polysome/40S) values across the available replicates.
- translation_initiation_efficiency_log2_sd
- Sample standard deviation of all QC-passing barcode-level log2 translation initiation efficiency (polysome/40S) values across the available replicates.
- translation_initiation_efficiency_log2_observations
- Number of barcode-by-replicate observations contributing to the translation initiation efficiency (polysome/40S) summary.
- qc_pass
- TRUE for reporter identities with at least three barcodes passing the package QC filter.
Quality control
The authors retained barcode observations with >10 reads in cDNA and plasmid pools and reported high replicate correlations for total RNA, polysome, and 40S measurements. The package additionally required >10 counts in both plasmid replicates and in every available total-RNA, polysome, and 40S replicate; reporter identities needed at least three retained barcodes. All 642 identities passed the reporter-level threshold. Failed barcode observations were excluded before mean-count and log2-ratio summaries were calculated.
Curation notes
Supplementary Data 1 contains 6,500 oligonucleotide/barcode designs for 642 reporter identities; Supplementary Data 2–5 contain plasmid, total-RNA, polysome, and 40S barcode counts. The Supplementary Data 5 description says four HeLa 40S replicates, but its workbook and the Methods contain two replicates; this package uses the two deposited 40S replicates. Count-table labels Lpcx1/Lpcx2/Lpcx4 were mapped to the sequence-table labels 7pcx1/7pcx2/7pcx4. The processed table is identity-level; complete barcode-level counts remain in raw_data.