Transient episomal TRE-MPRA of 6,144 detected synthetic promoter constructs in HEK293 cells, measuring serum and forskolin responses against untreated cells. The table combines public aggregate barcode RPM data with publisher MPRAnalyze statistics and baseline replicate values.
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
10% fetal bovine serum or 20 uM forskolin for 6 h; untreated serum-free comparator
Transient plasmid TRE-MPRA; synthetic TF motif units were paired with minCMV, minProm, or minTK promoters and drove Luc2 transcripts carrying 24-nt 3' UTR barcodes. RNA barcode abundance was compared with input plasmid DNA and analyzed with MPRAnalyze.
Processed data
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Visible columns (22 of 22)
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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 · 22 definitions
element_id
Unique synthetic promoter architecture label from the public RPM matrix.
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 sequence from Supplementary Data 3.
n_mapped_barcodes
Number of barcode-dictionary entries mapped to this promoter.
n_rpm_barcodes
Number of barcode rows for this promoter in the public RPM matrix.
baseline_log2_rna_dna_rep1
Publisher baseline log2 RNA/DNA value for HEK293 replicate experiment 1.
baseline_log2_rna_dna_rep2
Publisher baseline log2 RNA/DNA value for HEK293 replicate experiment 2.
fbs_lrt
Publisher MPRAnalyze likelihood-ratio statistic for FBS versus untreated.
fbs_pval
Publisher p-value for FBS versus untreated.
fbs_fdr
Publisher FDR for FBS versus untreated.
fbs_log2fc
Publisher log2 fold change for FBS versus untreated.
forskolin_lrt
Publisher MPRAnalyze likelihood-ratio statistic for forskolin versus untreated.
forskolin_pval
Publisher p-value for forskolin versus untreated.
forskolin_fdr
Publisher FDR for forskolin versus untreated.
forskolin_log2fc
Publisher log2 fold change for forskolin versus untreated.
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 requested title is the open-access bioRxiv preprint; its peer-reviewed update is linked in the parent metadata. Source data and the public GEO RPM matrix are from the same TRE-MPRA study and contain the final 6,144-promoter release.