Tet-Off promoter-shutoff 3′UTR RNA-stability MPRA
The quantitative impact of 3′UTRs on gene expressionThe 173-element pilot library was integrated into a HEK293T Tet-Off Bxb1 landing pad, pulsed without doxycycline for 4 hours, and then transcriptionally shut off with doxycycline. Barcode RNA was measured at 0, 1, 2, 3, 4, 8, and 20 hours alongside DNA and total-RNA reference libraries to quantify relative decay behavior.
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
4 h transcriptional pulse followed by 2 μg/mL doxycycline promoter shutoff
Targeted Bxb1 landing-pad integration of full-length 3′UTR GFP reporters carrying a 12-nt barcode. The release contains barcode CPMs for two replicates at seven post-shutoff timepoints, plus total-RNA and DNA libraries; the paper fits scaled time courses with an exponential/SSasymp-style model to obtain half-lives, but the qRT-PCR scaling factors are not included in the deposited count matrix.
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 · 20 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.
- dna_cpm_median
- Median across passing barcodes of mean normalized CPM from the two Tet-Off DNA replicates.
- total_rna_cpm_median
- Median across passing barcodes of mean normalized CPM from the two Tet-Off total-RNA reference replicates.
- steady_state_rna_abundance
- Median barcode-level total-RNA CPM divided by DNA CPM.
- log2_steady_state_rna_abundance
- Log2 of steady_state_rna_abundance.
- t00_cpm_median
- Median barcode CPM at 0 hours after doxycycline shutoff, averaged across the two biological replicates.
- t01_cpm_median
- Median barcode CPM at 1 hour after doxycycline shutoff, averaged across the two biological replicates.
- t02_cpm_median
- Median barcode CPM at 2 hours after doxycycline shutoff, averaged across the two biological replicates.
- t03_cpm_median
- Median barcode CPM at 3 hours after doxycycline shutoff, averaged across the two biological replicates.
- t04_cpm_median
- Median barcode CPM at 4 hours after doxycycline shutoff, averaged across the two biological replicates.
- t08_cpm_median
- Median barcode CPM at 8 hours after doxycycline shutoff, averaged across the two biological replicates.
- t20_cpm_median
- Median barcode CPM at 20 hours after doxycycline shutoff, averaged across the two biological replicates.
- t20_t00_ratio
- Median barcode-level ratio of the 20-hour CPM to the 0-hour CPM.
- log2_t20_t00_ratio
- Log2 of t20_t00_ratio.
- log2_decay_slope_per_hour
- Median per-barcode ordinary-least-squares slope of log2 time-course CPM versus hours 0, 1, 2, 3, 4, 8, and 20; negative values indicate decay. This is a package-derived relative metric, not the paper's scaled half-life.
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 DNA, total-RNA, and positive counts at every replicate/timepoint; 147 positions passed. Position-level values are medians across passing barcodes, and no significance-based effect filter was applied.
Curation notes
The paper reports a 173-UTR Tet-Off library, while the released linkage file contains 1,404 distinct position IDs; coverage QC leaves 147 rows. qRT-PCR-derived scaling factors used by the authors for half-life fitting are not present in GSE270252, so t20_t00_ratio and log2_decay_slope_per_hour are explicitly transparent relative metrics and should not be interpreted as the publication's exact half-life estimates.