Experiment / E1Q5VX3GRPromoter / Core Promoter MPRA

Cross-cell-line baseline and serum-response TRE-MPRA

Discovery and Validation of Context-Dependent Synthetic Mammalian Promoters

Transient episomal TRE-MPRA of the synthetic promoter library in HEK293, Neuro-2a, BHK-21, HeLa, MDA-MB-231, and A375 cells under serum-free and 10% FBS conditions. The table reports aggregate RNA/DNA and treatment/control values across cell lines plus publisher baseline and FBS comparisons.

Download processed table (CSV)Raw source data API documentation

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 or 10% FBS for 6 h across six mammalian cell lines

The host panel spans human, mouse, and hamster-derived cell lines; all constructs are synthetic promoter/Luc2 barcode reporters. Cell-line-specific input DNA columns were matched to the sequencing batch in the public matrix.

Processed data

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Visible columns (64 of 64)

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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_hek293_fbs: Sum of treatment-condition barcode RNA RPM values; suffix identifies the condition or cell line.
aggregate_control_rna_rpm_hek293_fbs: Sum of matched untreated/control barcode RNA RPM values.
aggregate_dna_rpm_hek293_fbs: Sum of input plasmid DNA RPM values for the matched sequencing batch.
aggregate_log2_rna_dna_hek293_fbs: Log2 of aggregate treatment RNA RPM divided by aggregate input DNA RPM.
aggregate_log2fc_hek293_fbs: Log2 of aggregate treatment RNA RPM divided by aggregate control RNA RPM.
aggregate_rna_rpm_n2a_fbs: Sum of treatment-condition barcode RNA RPM values; suffix identifies the condition or cell line.
aggregate_control_rna_rpm_n2a_fbs: Sum of matched untreated/control barcode RNA RPM values.
aggregate_dna_rpm_n2a_fbs: Sum of input plasmid DNA RPM values for the matched sequencing batch.
aggregate_log2_rna_dna_n2a_fbs: Log2 of aggregate treatment RNA RPM divided by aggregate input DNA RPM.
aggregate_log2fc_n2a_fbs: Log2 of aggregate treatment RNA RPM divided by aggregate control RNA RPM.
aggregate_rna_rpm_bhk_fbs: Sum of treatment-condition barcode RNA RPM values; suffix identifies the condition or cell line.
aggregate_control_rna_rpm_bhk_fbs: Sum of matched untreated/control barcode RNA RPM values.
aggregate_dna_rpm_bhk_fbs: Sum of input plasmid DNA RPM values for the matched sequencing batch.
aggregate_log2_rna_dna_bhk_fbs: Log2 of aggregate treatment RNA RPM divided by aggregate input DNA RPM.
aggregate_log2fc_bhk_fbs: Log2 of aggregate treatment RNA RPM divided by aggregate control RNA RPM.
aggregate_rna_rpm_hela_fbs: Sum of treatment-condition barcode RNA RPM values; suffix identifies the condition or cell line.
aggregate_control_rna_rpm_hela_fbs: Sum of matched untreated/control barcode RNA RPM values.
aggregate_dna_rpm_hela_fbs: Sum of input plasmid DNA RPM values for the matched sequencing batch.
aggregate_log2_rna_dna_hela_fbs: Log2 of aggregate treatment RNA RPM divided by aggregate input DNA RPM.
aggregate_log2fc_hela_fbs: Log2 of aggregate treatment RNA RPM divided by aggregate control RNA RPM.
aggregate_rna_rpm_mda_fbs: Sum of treatment-condition barcode RNA RPM values; suffix identifies the condition or cell line.
aggregate_control_rna_rpm_mda_fbs: Sum of matched untreated/control barcode RNA RPM values.
aggregate_dna_rpm_mda_fbs: Sum of input plasmid DNA RPM values for the matched sequencing batch.
aggregate_log2_rna_dna_mda_fbs: Log2 of aggregate treatment RNA RPM divided by aggregate input DNA RPM.
aggregate_log2fc_mda_fbs: Log2 of aggregate treatment RNA RPM divided by aggregate control RNA RPM.
aggregate_rna_rpm_a375_fbs: Sum of treatment-condition barcode RNA RPM values; suffix identifies the condition or cell line.
aggregate_control_rna_rpm_a375_fbs: Sum of matched untreated/control barcode RNA RPM values.
aggregate_dna_rpm_a375_fbs: Sum of input plasmid DNA RPM values for the matched sequencing batch.
aggregate_log2_rna_dna_a375_fbs: Log2 of aggregate treatment RNA RPM divided by aggregate input DNA RPM.
aggregate_log2fc_a375_fbs: Log2 of aggregate treatment RNA RPM divided by aggregate control RNA RPM.
source_hek293_sf1_log2: Publisher source-data value for the indicated baseline cell-line comparison.
source_hek293_sf2_log2: Publisher source-data value for the indicated baseline cell-line comparison.
source_n2a_sf_log2: Publisher source-data value for the indicated baseline cell-line comparison.
source_bhk_sf_log2: Publisher source-data value for the indicated baseline cell-line comparison.
source_hela_sf_log2: Publisher source-data value for the indicated baseline cell-line comparison.
source_mda_sf_log2: Publisher source-data value for the indicated baseline cell-line comparison.
source_a375_sf_log2: Publisher source-data value for the indicated baseline cell-line comparison.
publisher_a375_lrt: Publisher MPRAnalyze likelihood-ratio test statistic for the indicated comparison.
publisher_a375_fdr: Publisher multiple-testing-adjusted FDR for the indicated comparison.
publisher_a375_log2fc: Publisher log2 fold change for the indicated comparison.
publisher_bhk_lrt: Publisher MPRAnalyze likelihood-ratio test statistic for the indicated comparison.
publisher_bhk_fdr: Publisher multiple-testing-adjusted FDR for the indicated comparison.
publisher_bhk_log2fc: Publisher log2 fold change for the indicated comparison.
publisher_hela_lrt: Publisher MPRAnalyze likelihood-ratio test statistic for the indicated comparison.
publisher_hela_fdr: Publisher multiple-testing-adjusted FDR for the indicated comparison.
publisher_hela_log2fc: Publisher log2 fold change for the indicated comparison.
publisher_mda_lrt: Publisher MPRAnalyze likelihood-ratio test statistic for the indicated comparison.
publisher_mda_fdr: Publisher multiple-testing-adjusted FDR for the indicated comparison.
publisher_mda_log2fc: Publisher log2 fold change for the indicated comparison.
publisher_n2a_lrt: Publisher MPRAnalyze likelihood-ratio test statistic for the indicated comparison.
publisher_n2a_fdr: Publisher multiple-testing-adjusted FDR for the indicated comparison.
publisher_n2a_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

BHK-21 is hamster-derived and Neuro-2a is mouse-derived, so no single organism or biosample CURIE is assigned to this multi-line experiment.

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