Experiment / E6DEXPSJVTrans-Factor Perturbation MPRA

Aminergic GPCR agonism TRE-MPRA

Discovery and Validation of Context-Dependent Synthetic Mammalian Promoters

Transient episomal TRE-MPRA in HEK293 cells expressing aminergic GPCRs, with agonist-treated versus receptor-only controls. Aggregate barcode RPM-derived values are provided for DRD1, DRD2, HTR2A, and OPRM1, with publisher inferential results for the broader ADRB2/D1R/D2R/HTR2A/OPRM1 and endogenous ADRB2 comparisons.

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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

1 uM dopamine (DRD1/DRD2), 100 nM serotonin (HTR2A), or 100 nM morphine (OPRM1); receptor-only controls and ADRB2/eGFP epinephrine conditions are included in source data

The TRE-MPRA library was co-transfected with GPCR expression plasmids or control eGFP plasmid. RNA barcode abundance was compared with input DNA and receptor-only or matched control conditions; publisher statistics were generated with MPRAnalyze.

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 · 64 definitions

element_id: Unique synthetic promoter architecture label.
motif: TF binding motif or positive/negative control name.
neg_ctrl: Negative-control indicator from the source matrix (0/1).
tre: TRE motif-copy/configuration index used in the architecture label.
tre_unit_id: TRE-unit identifier from Supplementary Data 3.
promoter: Synthetic promoter design attribute recorded in the source architecture.
period: Synthetic promoter design attribute recorded in the source architecture.
spacer: Synthetic promoter design attribute recorded in the source architecture.
tre_unit_length_bp: TRE-unit length in base pairs from Supplementary Data 3.
tre_unit_sequence: Synthetic TRE-unit DNA sequence from Supplementary Data 3.
n_mapped_barcodes: Barcode-dictionary coverage for the promoter.
n_rpm_barcodes: Barcode-row coverage in the public RPM matrix.
aggregate_rna_rpm_drd1: Sum of treatment-condition barcode RNA RPM values; suffix identifies the condition or cell line.
aggregate_control_rna_rpm_drd1: Sum of matched untreated/control barcode RNA RPM values.
aggregate_dna_rpm_drd1: Sum of input plasmid DNA RPM values for the matched sequencing batch.
aggregate_log2_rna_dna_drd1: Log2 of aggregate treatment RNA RPM divided by aggregate input DNA RPM.
aggregate_log2fc_drd1: Log2 of aggregate treatment RNA RPM divided by aggregate control RNA RPM.
aggregate_rna_rpm_drd2: Sum of treatment-condition barcode RNA RPM values; suffix identifies the condition or cell line.
aggregate_control_rna_rpm_drd2: Sum of matched untreated/control barcode RNA RPM values.
aggregate_dna_rpm_drd2: Sum of input plasmid DNA RPM values for the matched sequencing batch.
aggregate_log2_rna_dna_drd2: Log2 of aggregate treatment RNA RPM divided by aggregate input DNA RPM.
aggregate_log2fc_drd2: Log2 of aggregate treatment RNA RPM divided by aggregate control RNA RPM.
aggregate_rna_rpm_htr2a: Sum of treatment-condition barcode RNA RPM values; suffix identifies the condition or cell line.
aggregate_control_rna_rpm_htr2a: Sum of matched untreated/control barcode RNA RPM values.
aggregate_dna_rpm_htr2a: Sum of input plasmid DNA RPM values for the matched sequencing batch.
aggregate_log2_rna_dna_htr2a: Log2 of aggregate treatment RNA RPM divided by aggregate input DNA RPM.
aggregate_log2fc_htr2a: Log2 of aggregate treatment RNA RPM divided by aggregate control RNA RPM.
aggregate_rna_rpm_oprm1: Sum of treatment-condition barcode RNA RPM values; suffix identifies the condition or cell line.
aggregate_control_rna_rpm_oprm1: Sum of matched untreated/control barcode RNA RPM values.
aggregate_dna_rpm_oprm1: Sum of input plasmid DNA RPM values for the matched sequencing batch.
aggregate_log2_rna_dna_oprm1: Log2 of aggregate treatment RNA RPM divided by aggregate input DNA RPM.
aggregate_log2fc_oprm1: Log2 of aggregate treatment RNA RPM divided by aggregate control RNA RPM.
adrb2_lrt: Publisher MPRAnalyze likelihood-ratio test statistic for the indicated comparison.
adrb2_pval: Publisher p-value for the indicated comparison.
adrb2_fdr: Publisher multiple-testing-adjusted FDR for the indicated comparison.
adrb2_log2fc: Publisher log2 fold change for the indicated comparison.
drd2_lrt: Publisher MPRAnalyze likelihood-ratio test statistic for the indicated comparison.
drd2_pval: Publisher p-value for the indicated comparison.
drd2_fdr: Publisher multiple-testing-adjusted FDR for the indicated comparison.
drd2_log2fc: Publisher log2 fold change for the indicated comparison.
htr2a_lrt: Publisher MPRAnalyze likelihood-ratio test statistic for the indicated comparison.
htr2a_pval: Publisher p-value for the indicated comparison.
htr2a_fdr: Publisher multiple-testing-adjusted FDR for the indicated comparison.
htr2a_log2fc: Publisher log2 fold change for the indicated comparison.
drd1_lrt: Publisher MPRAnalyze likelihood-ratio test statistic for the indicated comparison.
drd1_pval: Publisher p-value for the indicated comparison.
drd1_fdr: Publisher multiple-testing-adjusted FDR for the indicated comparison.
drd1_log2fc: Publisher log2 fold change for the indicated comparison.
oprm1_lrt: Publisher MPRAnalyze likelihood-ratio test statistic for the indicated comparison.
oprm1_pval: Publisher p-value for the indicated comparison.
oprm1_fdr: Publisher multiple-testing-adjusted FDR for the indicated comparison.
oprm1_log2fc: Publisher log2 fold change for the indicated comparison.
endogenous_epinephrine_lrt: Publisher MPRAnalyze likelihood-ratio test statistic for the indicated comparison.
endogenous_epinephrine_pval: Publisher p-value for the indicated comparison.
endogenous_epinephrine_fdr: Publisher multiple-testing-adjusted FDR for the indicated comparison.
endogenous_epinephrine_log2fc: Publisher log2 fold change for the indicated comparison.
adrb2_overexpression_lrt: Publisher MPRAnalyze likelihood-ratio test statistic for the indicated comparison.
adrb2_overexpression_pval: Publisher p-value for the indicated comparison.
adrb2_overexpression_fdr: Publisher multiple-testing-adjusted FDR for the indicated comparison.
adrb2_overexpression_log2fc: Publisher log2 fold change for the indicated comparison.
drd2_plus_epinephrine_lrt: Publisher MPRAnalyze likelihood-ratio test statistic for the indicated comparison.
drd2_plus_epinephrine_pval: Publisher p-value for the indicated comparison.
drd2_plus_epinephrine_fdr: Publisher multiple-testing-adjusted FDR for the indicated comparison.
drd2_plus_epinephrine_log2fc: Publisher log2 fold change for the indicated comparison.

Quality control

Retained elements with at least 5 barcodes in the final barcode dictionary and at least 5 barcode rows in the public RPM matrix; excluded empty/malformed elements and elements below either coverage threshold. The source study reports spike-in recovery QC with no sample failures, MPRAnalyze-based differential testing, and top-100 plasmid-abundance barcode selection for promoters with more than 100 barcodes. Publisher inferential columns are retained where the corresponding source-data sheet was available.

Curation notes

The public RPM matrix includes several related ADRB2 and D2R control/agonist columns; the aggregate columns focus on the receptor comparisons represented by the main aminergic GPCR analyses, while source inferential columns preserve additional publisher contrasts.

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