Experiment / E3SYV1NY43' UTR / RNA Stability MPRA (MPRAu)

PGK-promoter full-length human 3′UTR MPRA

The quantitative impact of 3′UTRs on gene expression

More than 1,400 full-length human 3′UTRs were integrated as single-copy barcoded GFP reporters in a HEK293T Bxb1 landing pad driven by the moderate PGK promoter. The experiment measures relative protein output by GFP-bin sorting, steady-state RNA abundance by RNA/DNA barcode ratios, and translational distribution by polysome profiling.

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: hg19
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Targeted Bxb1 landing-pad integration of a GFP reporter containing the PGK promoter, an EF1α 5′UTR intron, a 12-nt barcode, and a full-length 3′UTR extended 150 nt beyond the cleavage site. The deposited GSE270252 matrix contains five GFP FACS bins, total-DNA and total-RNA barcode CPMs, and cytoplasmic plus F1–F15 polysome fractions; the table summarizes the promoter-matched collections.

Processed data

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

Visible columns (32 of 32)

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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 · 32 definitions

element_id: Unique GEO position identifying the plate, well, and 3′UTR reporter.
gene: 3′UTR/gene token parsed from element_id.
plate: Source library plate.
well: Source 96-well position.
linked_barcode_count: Number of barcode linkages for this position in GSE270253.
qc_barcode_count: Number of linked barcodes retained after experiment-level coverage QC.
protein_score: Published protein output score computed from five FACS-bin CPMs with weights −2, −1, 0, +1, and +2, divided by the summed CPM.
protein_score_sd: Population SD of protein scores across QC-passing barcodes.
dna_cpm_median: Median normalized CPM in the promoter-matched total-genomic-DNA library.
rna_cpm_median: Median normalized CPM in the promoter-matched total-RNA library.
rna_abundance_ratio: Median barcode-level RNA CPM divided by DNA CPM.
log2_rna_abundance: Log2 of rna_abundance_ratio.
translation_score_fraction_index: Median barcode-level polysome translation proxy using fraction-index weights cyt=0, F1=1, through F15=15.
translation_score_fraction_index_sd: Population SD of the polysome fraction-index proxy across QC-passing barcodes.
polysome_dna_cpm_median: Median normalized CPM in the DNA library matched to the polysome collection.
polysome_total_cpm_median: Median across barcodes of the summed CPM from the cytoplasmic/input and F1–F15 polysome samples.
polysome_cpm_cyt: Median normalized CPM in the cytoplasmic/input polysome sample.
polysome_cpm_F1: Median normalized CPM in polysome fraction F1.
polysome_cpm_F2: Median normalized CPM in polysome fraction F2.
polysome_cpm_F3: Median normalized CPM in polysome fraction F3.
polysome_cpm_F4: Median normalized CPM in polysome fraction F4.
polysome_cpm_F5: Median normalized CPM in polysome fraction F5.
polysome_cpm_F6: Median normalized CPM in polysome fraction F6.
polysome_cpm_F7: Median normalized CPM in polysome fraction F7.
polysome_cpm_F8: Median normalized CPM in polysome fraction F8.
polysome_cpm_F9: Median normalized CPM in polysome fraction F9.
polysome_cpm_F10: Median normalized CPM in polysome fraction F10.
polysome_cpm_F11: Median normalized CPM in polysome fraction F11.
polysome_cpm_F12: Median normalized CPM in polysome fraction F12.
polysome_cpm_F13: Median normalized CPM in polysome fraction F13.
polysome_cpm_F14: Median normalized CPM in polysome fraction F14.
polysome_cpm_F15: Median normalized CPM in polysome fraction F15.

Quality control

The deposited linkage map contains 4,245 barcode records across 1,404 library positions. This package retained positions with at least two linked barcodes and at least two barcodes having positive summed FACS counts, positive promoter-matched DNA and RNA CPMs, and positive summed polysome counts; 1,383 positions passed. All reported values are median summaries across passing barcodes, preserving internal barcode replication without applying a significance-based effect filter.

Curation notes

The article reports 1,401 3′UTRs, while the released linkage table has 1,404 distinct position IDs; this package retains the released IDs and documents the distinction. The released counts do not include an independent ribosome-number vector, so translation_score_fraction_index is a reproducible fraction-index proxy and the component fraction CPMs are retained. The table uses promoter-matched samples from GSE270252 and does not infer genomic coordinates for individual UTRs.

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