9×9 enhancer–core promoter matrix: single-cell flow-cytometry noise assay
Permutational analysis of Saccharomyces cerevisiae regulatory elementsThe same 81-construct episomal reporter matrix was measured in glucose-containing medium by flow cytometry across three biological replicates. Per-construct mean fluorescence and dispersion summaries were used to quantify expression and expression noise.
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.
Perturbation & assay details
Basal / Glucose-rich YMD medium
Nine UAS enhancers were crossed with nine core promoters and their associated 5′ UTR modules; the PGK1 3′ UTR/terminator was constant. The raw repository provides rep1–rep3 mean_nolog and std_nolog 9×9 CSV matrices plus a MATLAB data.mat file. The processed Fano and CV² values are derived as std²/mean and std²/mean² from the supplied mean/std CSVs.
Arrayed episomal fluorescent reporter matrix without barcode sequencing: single-cell Venus fluorescence was measured by flow cytometry for each construct and summarized by mean and standard deviation.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 17 definitions
- enhancer_uas
- UAS enhancer identity; matrix order is TDH3, PGK1, PDC1, ACO1, RPL28, TPI1, ICL1, LEU9, ADE2.
- core_promoter
- Core promoter identity in the same 9-element matrix order.
- mean_expression_rep1_au
- Source replicate 1 mean fluorescence in the nolog matrix, arbitrary units.
- mean_expression_rep2_au
- Source replicate 2 mean fluorescence in the nolog matrix, arbitrary units.
- mean_expression_rep3_au
- Source replicate 3 mean fluorescence in the nolog matrix, arbitrary units.
- mean_expression_mean_au
- Arithmetic mean of the three supplied replicate mean-fluorescence values.
- between_replicate_sd_au
- Sample standard deviation across the three supplied replicate mean-fluorescence values.
- std_expression_rep1_au
- Source replicate 1 standard deviation of single-cell fluorescence, arbitrary units.
- std_expression_rep2_au
- Source replicate 2 standard deviation of single-cell fluorescence, arbitrary units.
- std_expression_rep3_au
- Source replicate 3 standard deviation of single-cell fluorescence, arbitrary units.
- fano_rep1_derived
- Derived replicate 1 Fano factor, std_expression_rep1_au² / mean_expression_rep1_au.
- fano_rep2_derived
- Derived replicate 2 Fano factor, std_expression_rep2_au² / mean_expression_rep2_au.
- fano_rep3_derived
- Derived replicate 3 Fano factor, std_expression_rep3_au² / mean_expression_rep3_au.
- fano_mean_derived
- Arithmetic mean of the three derived Fano factors.
- cv2_mean_derived
- Arithmetic mean of the three derived squared coefficients of variation, std² / mean².
- biological_replicate_count
- Number of supplied biological replicate matrices summarized, three.
- qc_pass
- TRUE for a complete finite 9×9 construct retained after removal of source padding.
Quality control
The public notebook uses the first 9×9 entries of the source matrices; the raw standard-deviation CSVs contain an additional trailing all-NaN row and column, which were excluded as padding. All 81 enhancer–promoter pairs had finite nonnegative mean and standard-deviation values in all three replicates, so 81 rows passed QC.
Curation notes
The assayed cells were the W-303 derivative ROY5634 and the reference assembly was not stated. The matrix order follows the source notebook rather than lexical gene order. The standard-deviation CSVs contain a trailing all-NaN padding row and column; this package uses the first 9×9 values, matching the notebook's matrix slice. Fano and CV² are explicitly package-derived from the supplied nolog mean/std matrices and should not be confused with the main sort-seq activity scores.