Experiment / E76LG2CLBTrans-Factor Perturbation MPRA

Non-aminergic and promiscuous GPCR TRE-MPRA

Discovery and Validation of Context-Dependent Synthetic Mammalian Promoters

Transient episomal TRE-MPRA in HEK293 cells expressing PAR1, GPR91, MRGPRX2, or NTSR1, including NTSR1 agonism with Gq inhibition. Aggregate barcode RPM-derived treatment/control values are joined to publisher inferential statistics and biplot coordinates where available.

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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

30 uM cis-epoxy-succinate (GPR91), 10 nM thrombin (PAR1), 3 uM (R)-zn3573 (MRGPRX2), or 100 nM neurotensin 8-13 with or without 50 nM FR900359 (NTSR1)

HEK293 cells were co-transfected with the TRE-MPRA library and GPCR expression plasmids. NTSR1 was also assayed after Gq-pathway inhibition with FR900359; publisher MPRAnalyze results and public aggregate RPM values are retained.

Processed data

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Column dictionary · 59 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_gpr91: Sum of treatment-condition barcode RNA RPM values; suffix identifies the condition or cell line.
aggregate_control_rna_rpm_gpr91: Sum of matched untreated/control barcode RNA RPM values.
aggregate_dna_rpm_gpr91: Sum of input plasmid DNA RPM values for the matched sequencing batch.
aggregate_log2_rna_dna_gpr91: Log2 of aggregate treatment RNA RPM divided by aggregate input DNA RPM.
aggregate_log2fc_gpr91: Log2 of aggregate treatment RNA RPM divided by aggregate control RNA RPM.
aggregate_rna_rpm_par1: Sum of treatment-condition barcode RNA RPM values; suffix identifies the condition or cell line.
aggregate_control_rna_rpm_par1: Sum of matched untreated/control barcode RNA RPM values.
aggregate_dna_rpm_par1: Sum of input plasmid DNA RPM values for the matched sequencing batch.
aggregate_log2_rna_dna_par1: Log2 of aggregate treatment RNA RPM divided by aggregate input DNA RPM.
aggregate_log2fc_par1: Log2 of aggregate treatment RNA RPM divided by aggregate control RNA RPM.
aggregate_rna_rpm_mrgprx2: Sum of treatment-condition barcode RNA RPM values; suffix identifies the condition or cell line.
aggregate_control_rna_rpm_mrgprx2: Sum of matched untreated/control barcode RNA RPM values.
aggregate_dna_rpm_mrgprx2: Sum of input plasmid DNA RPM values for the matched sequencing batch.
aggregate_log2_rna_dna_mrgprx2: Log2 of aggregate treatment RNA RPM divided by aggregate input DNA RPM.
aggregate_log2fc_mrgprx2: Log2 of aggregate treatment RNA RPM divided by aggregate control RNA RPM.
aggregate_rna_rpm_ntsr1: Sum of treatment-condition barcode RNA RPM values; suffix identifies the condition or cell line.
aggregate_control_rna_rpm_ntsr1: Sum of matched untreated/control barcode RNA RPM values.
aggregate_dna_rpm_ntsr1: Sum of input plasmid DNA RPM values for the matched sequencing batch.
aggregate_log2_rna_dna_ntsr1: Log2 of aggregate treatment RNA RPM divided by aggregate input DNA RPM.
aggregate_log2fc_ntsr1: Log2 of aggregate treatment RNA RPM divided by aggregate control RNA RPM.
aggregate_rna_rpm_ntsr1_gq_inhibitor: Sum of treatment-condition barcode RNA RPM values; suffix identifies the condition or cell line.
aggregate_control_rna_rpm_ntsr1_gq_inhibitor: Sum of matched untreated/control barcode RNA RPM values.
aggregate_dna_rpm_ntsr1_gq_inhibitor: Sum of input plasmid DNA RPM values for the matched sequencing batch.
aggregate_log2_rna_dna_ntsr1_gq_inhibitor: Log2 of aggregate treatment RNA RPM divided by aggregate input DNA RPM.
aggregate_log2fc_ntsr1_gq_inhibitor: Log2 of aggregate treatment RNA RPM divided by aggregate control RNA RPM.
par1_lrt: Publisher MPRAnalyze likelihood-ratio test statistic for the indicated comparison.
par1_pval: Publisher p-value for the indicated comparison.
par1_fdr: Publisher multiple-testing-adjusted FDR for the indicated comparison.
par1_log2fc: Publisher log2 fold change for the indicated comparison.
gpr91_lrt: Publisher MPRAnalyze likelihood-ratio test statistic for the indicated comparison.
gpr91_pval: Publisher p-value for the indicated comparison.
gpr91_fdr: Publisher multiple-testing-adjusted FDR for the indicated comparison.
gpr91_log2fc: Publisher log2 fold change for the indicated comparison.
mrgprx2_lrt: Publisher MPRAnalyze likelihood-ratio test statistic for the indicated comparison.
mrgprx2_pval: Publisher p-value for the indicated comparison.
mrgprx2_fdr: Publisher multiple-testing-adjusted FDR for the indicated comparison.
mrgprx2_log2fc: Publisher log2 fold change for the indicated comparison.
ntsr1_lrt: Publisher MPRAnalyze likelihood-ratio test statistic for the indicated comparison.
ntsr1_pval: Publisher p-value for the indicated comparison.
ntsr1_fdr: Publisher multiple-testing-adjusted FDR for the indicated comparison.
ntsr1_log2fc: Publisher log2 fold change for the indicated comparison.
ntsr1_gq_inhibitor_lrt: Publisher MPRAnalyze likelihood-ratio test statistic for the indicated comparison.
ntsr1_gq_inhibitor_pval: Publisher p-value for the indicated comparison.
ntsr1_gq_inhibitor_fdr: Publisher multiple-testing-adjusted FDR for the indicated comparison.
ntsr1_gq_inhibitor_log2fc: Publisher log2 fold change for the indicated comparison.
gpcr_biplot_x: Publisher biplot x-coordinate for the NTSR1 source comparison when available.
gpcr_biplot_y: Publisher biplot y-coordinate for the NTSR1 source comparison when available.

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 NTSR1 + FR900359 columns use the public gqinh_23820 and ntsr1_23820 RPM fields and correspond to the Gq-inhibitor comparison in the publisher source data.

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