Experiment / E2PUQYEOAPromoter / Core Promoter MPRA

Baseline activity of yeast UAS–core-promoter combinations

Broad compatibility between yeast UAS elements and core promoters and identification of promoter elements that determine cofactor specificity

An episomal, barcoded plasmid MPRA tested approximately 4,200 genomic yeast UASs and 222 genomic control sequences upstream of four representative yeast core promoters. This long-format table contains the published baseline reporter-expression summary for each element–core-promoter pair.

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: Budding yeast
Taxonomy ID: NCBITaxon:4932
Biosample: UNMAPPED:Saccharomyces_cerevisiae_BY4705-derived_degron_strains
Reference genome: Not reported / not applicable
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / no auxin (DMSO vehicle)

Episomal yeast reporter plasmids were derived from Yeast_Dual_Reporter (Addgene plasmid 127546) with unstable GFP. Each library contained a 199–200 nt UAS/control sequence upstream of one of four 60 nt TFIIB-defined core-promoter regions (SIT1, KRS1, NOP13, or RPC10), followed by a G-less randomized 18 nt barcode in the uGFP 5′ UTR. Nascent RNA was labeled with 4-thiouracil for 5 min, targeted barcode RNA sequencing was paired with DNA plasmid-library sequencing, and RNA barcode counts were normalized to DNA input. The published expression values are aggregate processed reporter measurements rather than raw read counts.

Processed data

50 rows per page. Click a cell to inspect its full value.

Visible columns (32 of 32)

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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 · 32 definitions

source_table_row: 1-based row number of the source Table S1 worksheet.
element_id: Yeast gene identifier for a UAS or identifier for a genomic control sequence.
sequence_type: Source category: UAS, accessible control, or inaccessible control.
element_sequence: DNA sequence of the tested UAS or control element as reported in Table S1.
sequence_length_bp: Length of element_sequence in base pairs.
chromosome: Yeast chromosome for the element or control assignment from the authors' reference tables.
region_start: 1-based genomic start coordinate from the authors' reference tables.
region_end: 1-based genomic end coordinate from the authors' reference tables.
strand: Reported orientation of the tested sequence (+ or −).
coordinate_source: Reference file used to add genomic coordinates.
faire_score: FAIRE accessibility score for genomic control sequences; blank for UAS rows.
control_bin: Authors' genomic control-region bin identifier; blank for UAS rows.
control_type: Authors' control type code; blank for UAS rows.
genomic_tail_dependence: Endogenous cofactor-tail dependence class associated with the source gene.
genomic_class: Endogenous regulatory class associated with the source gene: CR or TFIID.
genomic_tata_in_promoter: Endogenous promoter TATA annotation: strong, weak, none, or NA.
genomic_med8_chec: Whether the source UAS had detectable genomic Med8 ChEC-seq signal.
genomic_expression: Endogenous expression value associated with the source gene in the authors' reference data.
genomic_med15_depletion_log2fc: Endogenous genomic log2 fold change after Med15 depletion from the reference dataset.
genomic_spt7_depletion_log2fc: Endogenous genomic log2 fold change after Spt7 depletion from the reference dataset.
genomic_taf13_depletion_log2fc: Endogenous genomic log2 fold change after Taf13 depletion from the reference dataset.
core_promoter: Core-promoter reporter context: SIT1, KRS1, NOP13, or RPC10.
core_promoter_class: Regulatory class of the tested core promoter: CR or TFIID.
core_promoter_tail_dependence: Tail-dependence annotation of the core promoter: tail-dependent, tail-independent, or NA.
core_promoter_type: Core-promoter architecture annotation: TATA-containing or GA-element-containing.
reporter_expression: Published normalized reporter expression for the element–core-promoter pair, in the source table's scaled activity units; not a log2 value.
paper_qc_pass: TRUE for rows retained from the paper's final processed Table S1 after presence/QC filtering.
reporter_kmeans_cluster: Published K-means activity cluster for the element across the four promoter contexts.
reporter_core_class_activation_ratio: Published log ratio comparing activity at CR versus TFIID core promoters.
reporter_interreplicate_variance: Published variance of reporter activity across experimental batches/replicates.
uas_promoter_variance: Published variance of activity for the element across the four core-promoter contexts.
reporter_variance_class: Published reporter variance class: Low, Intermediate, or High.

Quality control

The study transformed each library at least tenfold above library complexity. Paired-end reads were joined and clustered at 99% similarity for RNA barcode amplicons and 97% similarity for DNA plasmid amplicons; DNA clusters were assigned to UAS/core references by fuzzy sequence matching and RNA barcodes by exact matching. Within each sample, only the most common DNA sequence for each barcode was retained, and barcodes assigned to more than one UAS–core context were removed. Reporter expression was calculated from library-size-normalized RNA divided by library-size-normalized DNA; normalized barcode counts had Pearson reproducibility of 0.71–0.97 across replicates. For this package, rows were retained from the published Table S1 only when the element sequence and requested reporter-expression endpoint were present; all retained rows are marked paper_qc_pass=TRUE.

Curation notes

The source Table S1 contains 4,464 unique elements (4,242 UASs, 112 accessible controls, and 110 inaccessible controls), represented here as four rows per element. The Table S1 UAS_sequence values are 199 nt for genomic UAS entries although the methods describe 200 nt UASs; values were preserved verbatim. Seven auxiliary Reporter_core_class_activation_ratio cells are Excel error values (#NAME?) in the source workbook; they are blank in processed_data because the primary reporter-expression endpoints remain valid, while the source workbook and lossless CSV retain the original values. The baseline endpoint is the published aggregate expression summary and does not expose strain-specific raw barcode counts. Coordinates were joined by exact sequence to UAS_reference_table.csv for UASs and by element_id to UAS_control_region_assignments.csv for controls; all 17,856 element–promoter rows mapped successfully.

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