Pilot Tet-On landing-pad 3′UTR FACS MPRA
The quantitative impact of 3′UTRs on gene expressionThe pilot library of 173 full-length human 3′UTRs was integrated as single-copy Bxb1 GFP reporters in a HEK293T Tet-On landing pad and sorted into five GFP bins in two independent runs. Barcode CPMs were used to summarize protein output, RNA/DNA abundance, and polysome-associated translation for each 3′UTR.
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
2 μg/mL doxycycline (Tet-On)
Targeted Bxb1 landing-pad integration of GFP reporters with a 12-nt barcode immediately downstream of the GFP stop codon and full-length 3′UTR plus 150 nt downstream genomic sequence. Protein output was measured by five-bin GFP FACS sorting in two pilot runs; matched barcode CPM data also support RNA/DNA abundance and polysome profiling, with fraction labels retained in the table.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (35 of 35)
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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 · 35 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_rep1
- Protein output score for pilot FACS replicate 1, computed as the weighted five-bin average scaled from −2 to +2.
- protein_score_rep2
- Protein output score for pilot FACS replicate 2, computed as the weighted five-bin average scaled from −2 to +2.
- protein_score_mean
- Per-barcode mean of the two protein scores, summarized as the median across passing barcodes.
- protein_score_sd
- Population SD across passing barcodes of the per-barcode mean protein score.
- dna_cpm_rep1
- Normalized barcode CPM in pilot genomic-DNA replicate 1.
- dna_cpm_rep2
- Normalized barcode CPM in pilot genomic-DNA replicate 2.
- dna_cpm_median
- Median across passing barcodes of the two-replicate mean DNA CPM.
- rna_cpm_rep1
- Normalized barcode CPM in pilot RNA replicate 1.
- rna_cpm_rep2
- Normalized barcode CPM in pilot RNA replicate 2.
- rna_cpm_rep3
- Normalized barcode CPM in pilot RNA replicate 3.
- rna_cpm_median
- Median across passing barcodes of the three-replicate mean RNA CPM.
- rna_abundance_ratio
- Median barcode-level RNA CPM divided by DNA CPM.
- log2_rna_abundance
- Log2 of rna_abundance_ratio.
- translation_score_fraction_index_rep1
- Polysome translation proxy for pilot replicate 1, using fraction-index weights cyt=0, F6=6, F10=10, F13=13, F16=16, and F18=18.
- translation_score_fraction_index_rep2
- Polysome translation proxy for pilot replicate 2, using fraction-index weights cyt=0, F8=8, F12=12, F15=15, F18=18, and F20=20.
- translation_score_fraction_index_mean
- Per-barcode mean of the two polysome fraction-index proxies, summarized as the median across passing barcodes.
- translation_score_fraction_index_sd
- Population SD across passing barcodes of the per-barcode mean polysome fraction-index proxy.
- polysome_rep1_cpm_cyt
- Normalized barcode CPM in the pilot replicate 1 cytoplasmic/input sample.
- polysome_rep1_cpm_F6
- Normalized barcode CPM in pilot replicate 1 polysome fraction F6.
- polysome_rep1_cpm_F10
- Normalized barcode CPM in pilot replicate 1 polysome fraction F10.
- polysome_rep1_cpm_F13
- Normalized barcode CPM in pilot replicate 1 polysome fraction F13.
- polysome_rep1_cpm_F16
- Normalized barcode CPM in pilot replicate 1 polysome fraction F16.
- polysome_rep1_cpm_F18
- Normalized barcode CPM in pilot replicate 1 polysome fraction F18.
- polysome_rep2_cpm_cyt
- Normalized barcode CPM in the pilot replicate 2 cytoplasmic/input sample.
- polysome_rep2_cpm_F8
- Normalized barcode CPM in pilot replicate 2 polysome fraction F8.
- polysome_rep2_cpm_F12
- Normalized barcode CPM in pilot replicate 2 polysome fraction F12.
- polysome_rep2_cpm_F15
- Normalized barcode CPM in pilot replicate 2 polysome fraction F15.
- polysome_rep2_cpm_F18
- Normalized barcode CPM in pilot replicate 2 polysome fraction F18.
- polysome_rep2_cpm_F20
- Normalized barcode CPM in pilot replicate 2 polysome fraction F20.
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 counts for both protein-score replicate profiles, RNA/DNA measurements, and both polysome profiles; 148 positions passed. Summaries are medians across passing barcodes, and no significance-based effect filter was applied.
Curation notes
The paper describes a 173-UTR pilot, whereas the released barcode linkage file contains 1,404 position identifiers spanning the study library; coverage QC leaves 148 table rows. The released matrix does not include a separate ribosome-number vector, so translation_score_fraction_index_* are transparent fraction-index proxies and the underlying fraction CPMs are retained. hg19 is recorded for the study's genomic annotation context; the table itself is keyed by library positions rather than genomic coordinates.