The TRE-MPRA library was used in HEK293 cells to profile transcriptional responses associated with nine GPCRs: ADRB2, DRD1, DRD2, HTR2A, OPRM1, PAR1, GPR91, MRGPRX2, and NTSR1. Receptor-expression controls, agonist treatments, endogenous ADRB2 stimulation, and NTSR1 signaling inhibition are represented as separate condition rows.
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:0045
Reference genome
Not reported / not applicable
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
GPCR overexpression and agonist stimulation with epinephrine, dopamine, serotonin, morphine, thrombin, cis-epoxysuccinate, (R)-zn3573, or neurotensin; NTSR1 signaling was also tested with FR900359 Gq inhibition
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, with 5 micrograms of a GPCR expression plasmid where indicated, 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
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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 contains nine GPCR contexts, with receptor-only and agonist conditions kept separate so receptor expression effects are not conflated with ligand responses. Most conditions are single replicates; GPR91 no-drug/agonist has three replicates, and the eGFP vector control has two. The NTSR1 plus neurotensin plus FR900359 condition is compared to ntsr1_23820 in the computed fold-change because the publisher Figure 5C comparison uses the NTSR1 no-drug control. The GEO SOFT metadata spells one GPR91 control key as gpr91nodrub_19664, whereas the RPM matrix uses gpr91nodrug_19664; the latter is retained in the table.