Experiment / E7EDW0LVFOther

9×9 enhancer–core promoter matrix under environmental and chromatin-factor conditions

Permutational analysis of Saccharomyces cerevisiae regulatory elements

An arrayed matrix of 81 episomal reporter constructs combined nine UAS enhancers with nine core promoter/5′ UTR modules and a constant PGK1 3′ UTR/terminator. Venus fluorescence was measured with a microtiter plate reader across carbon-source, adenine-depletion, chromatin-factor mutant and temperature-shift conditions.

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Organism: NCBITaxon:580240
Taxonomy ID: NCBITaxon:580240
Biosample: UNMAPPED:W-303 yeast strain ROY5634
Reference genome: Not reported / not applicable
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Multiple: glucose, galactose, glycerol, adenine depletion, Isw2Δ, Rsc2Δ and Mot1-1 32°C/4 h conditions

The nine UAS enhancers and nine core promoter/5′ UTR modules were tested as 81 combinations with the PGK1 3′ UTR/transcription terminator. Source run labels E1–E3 and condition labels are retained. The public analysis computed I_V = max(Intensity − Vector, 0), then normalized each source run/replicate/condition to total and maximum background-corrected signal; promoter- and enhancer-centered z-scores were also computed.

Arrayed episomal plasmid reporter matrix without barcode sequencing: individual Venus reporter constructs were measured by a microtiter fluorometer after subtraction of a vector/background fluorescence measurement.

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

source_run: Source repository run label from the Experiment column (E1, E2 or E3).
condition: Growth, genotype or temperature condition label retained from the source file.
enhancer_uas: UAS enhancer identity in the 9×9 matrix.
core_promoter: Core promoter identity in the 9×9 matrix; its matched 5′ UTR module was included in the construct.
replicate_count: Number of source biological replicate measurements summarized in the row.
replicate_ids: Semicolon-separated source replicate labels included in the summary.
intensity_mean_au: Mean raw Venus-associated plate-reader intensity across replicates.
intensity_sd_au: Sample standard deviation of raw plate-reader intensity across replicates.
vector_mean_au: Mean vector/background fluorescence across replicates.
vector_sd_au: Sample standard deviation of vector/background fluorescence across replicates.
background_subtracted_mean_au: Mean of max(Intensity − Vector, 0) across replicates.
background_subtracted_sd_au: Sample standard deviation of max(Intensity − Vector, 0) across replicates.
sum_normalized_percent_mean: Mean replicate-level background-corrected intensity normalized to the sum of all 81 constructs in the same source run/replicate/condition, expressed as percent.
sum_normalized_percent_sd: Sample standard deviation of the replicate-level sum-normalized percentages.
max_normalized_percent_mean: Mean replicate-level background-corrected intensity normalized to the maximum of all 81 constructs in the same source run/replicate/condition, expressed as percent.
max_normalized_percent_sd: Sample standard deviation of the replicate-level maximum-normalized percentages.
promoter_zscore_mean: Mean replicate-level z-score across enhancers for the same promoter, using background-corrected intensity.
promoter_zscore_sd: Sample standard deviation of promoter-centered z-scores across replicates.
enhancer_zscore_mean: Mean replicate-level z-score across promoters for the same enhancer, using background-corrected intensity.
enhancer_zscore_sd: Sample standard deviation of enhancer-centered z-scores across replicates.
negative_background_difference_count: Number of replicates where raw Intensity − Vector was negative and therefore clipped to zero.
qc_pass: TRUE for a complete source-run/condition/construct group retained after replicate and numeric-value QC.

Quality control

The raw matrix contains 2,268 finite observations across 729 source-run/condition/construct groups: 81 constructs for each of six E1 conditions, two E2 conditions and one E3 condition. All groups had at least three replicates and passed completeness QC; 729 rows were retained. The source analysis clipped 212 negative Intensity − Vector values to zero before normalization, rather than treating those measurements as missing. E1 and E2 groups have three replicates, while E3/Glucose has four source replicates.

Curation notes

This is the paper's arrayed 81-construct validation/readout rather than the barcode-linked main sort-seq library, so assay_type is recorded as Other. The source file's E1–E3 run semantics are not further defined in the repository; they are preserved as source_run. The paper describes triplicate measurements for the matrix, but the deposited E3/Glucose run has four replicates and no value was discarded or imputed. The matrix contains no sequence-level barcodes or DNA/RNA count ratio.

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