The barcoded TRE-MPRA library was transiently transfected into HEK293 cells for serum-free baseline, fetal bovine serum, and forskolin comparisons, and into five additional mammalian cell lines for serum-free versus fetal bovine serum benchmarking. The processed table retains promoter-level RNA/DNA activity for every available condition and cell-line context.
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
Not reported
Taxonomy ID
Not reported / not applicable
Biosample
Not reported / not applicable
Reference genome
Not reported / not applicable
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Serum-free baseline, 10% fetal bovine serum, and 20 uM forskolin across HEK293, Neuro2a, A375, MDA-MB-231, HeLa, and BHK-21
Transient episomal TRE-MPRA plasmids contained four copies of a TF motif in one of six TRE-unit configurations upstream of minCMV, minProm, or minTK and drove a Luc2 transcript with a 24-nt 3-prime UTR barcode. Cells were transfected for approximately 24 h, stimulated for 6 h, and assayed by sequencing barcode-containing RNA alongside input plasmid DNA. The public GEO matrix contains condition-level per-barcode RPM values; promoter activity in this package is the summed RNA RPM divided by summed DNA RPM for the same architecture and condition.
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 · 43 definitions
element_id
Stable package identifier for a synthetic promoter architecture
architecture
Original TRE-MPRA architecture descriptor
tre_id
Numeric synthetic TRE-unit identifier
tre_unit_class
TRE-unit category from Supplementary Data 3, such as candidate or negative control
motif
Transcription-factor motif label
motif_sequence
Motif sequence used in the TRE unit
tre_unit_sequence
Full sequence of the four-copy TRE unit and spacers
tre_unit_length_bp
TRE-unit sequence length in base pairs
promoter
Minimal promoter paired with the TRE unit
rotation_period
Helical rotation/phase setting for the TRE unit
spacer_set
Spacer sequence set used in the architecture
negative_control
Whether the architecture is a negative-control construct
barcode_count_in_rpms
Number of barcode rows available for this architecture in the GEO RPM matrix
condition_key
Condition column key in the GEO RPM matrix
condition_label
Human-readable condition label
condition_role
Role of the condition, such as baseline, treatment, or control
comparison_id
Treatment-versus-control comparison represented by the row, when applicable
cell_line
Cell line used for the condition
target_organism
NCBI Taxonomy CURIE for the cell line organism
biosample_id
Cellosaurus CURIE for the cell line
perturbation
Treatment or transfection context
dose
Applied treatment concentration, when stated
duration
Treatment duration
geo_sample_ids
GEO GSM accessions contributing to the condition
replicate_count
Number of GEO samples/biological replicates represented
dna_library
Input plasmid DNA library column used for normalization
n_barcodes_dna_present
Architecture barcodes with a numeric DNA RPM value
n_barcodes_dna_positive
Architecture barcodes with DNA RPM greater than zero
n_barcodes_rna_present
Architecture barcodes with a numeric RNA RPM value
n_barcodes_rna_positive
Architecture barcodes with RNA RPM greater than zero
dna_rpm_sum
Sum of DNA RPM across the architecture barcodes
rna_rpm_sum
Sum of RNA RPM across the architecture barcodes
activity_ratio_rna_dna
Promoter activity estimate calculated as summed RNA RPM divided by summed DNA RPM
log2_activity
Base-2 logarithm of activity_ratio_rna_dna
control_condition_key
Condition key used as the activity control, when applicable
aggregate_log2fc_vs_control
Base-2 log fold-change of the computed activity relative to the matched control condition
reported_lrt
Likelihood-ratio statistic copied from publisher Source Data when available
reported_pval
Publisher-reported p-value when available
reported_fdr
Publisher-reported false-discovery rate when available
reported_fdr_pass_5pct
Whether reported_fdr is at or below 0.05
reported_log2fc
Publisher-reported log2 fold-change when available
reported_source
Publisher figure/source-data sheet for reported statistics
qc_pass
Package-level QC flag; true for every retained row
Quality control
The study assessed library representation across four independent plasmid preparations, used RNA spike-ins to flag samples with poor barcode recovery, matched barcode/TRE sequences with Starcode and dictionary filters, and reported no excluded samples. This package additionally retained only rows with nonblank architecture annotations, numeric DNA/RNA entries, and positive summed DNA RPM; all retained rows are marked qc_pass=true. Publisher comparative statistics used MPRAnalyze with upper-quartile read-depth scaling and up to 100 highest-abundance DNA barcodes for promoters with more than 100 associated barcodes.
Curation notes
This panel combines related benchmark runs into one tidy table; row-level cell-line, taxonomy, and biosample fields preserve the mixed biological contexts. The two HEK293 serum-free groups use independent plasmid input batches 19664 and 19919; the non-HEK conditions are single-replicate GEO groups. Per-promoter statistics were copied from Figure 2 for HEK293 FBS/forskolin and Supplementary Figure S8 for the additional cell lines; conditions without an exact per-promoter source sheet retain the computed RPM-derived activity values only. Sequences are entirely synthetic, so reference_genome and region_of_interest are null.