A 48-construct synthetic promoter library tested combinations of Tye7p, Gcr1/2p, and Rap1p motif mutations in BMH1- and TDH3-derived promoters. The same reporter-array library provided Tye7p/Gcr1p/Gcr2p CCRA binding scores and eight-bin fluorescence-sorted Sort-Seq reporter expression 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
Budding yeast
Taxonomy ID
NCBITaxon:4932
Biosample
UNMAPPED:yRM1004
Reference genome
Not reported / not applicable
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
No exogenous treatment stated for the Sort-Seq reporter-expression branch; galactose-induced Ty5 transposition was used for companion CCRA binding measurements
The pRM1806 episomal library plasmid placed each 170-bp synthetic promoter upstream of YFP and expressed constitutive mCherry from the same vector for internal normalization. For the expression branch, transformed yeast were sorted into eight bins of 100,000 cells, each bin was sequenced, and the author-provided expression(A.U.) values were calculated from barcode abundance across bins. Companion CCRA binding used TF-Sir4p-directed Ty5 insertion and reported NBS for Tye7p, Gcr1p, and Gcr2p.
Processed data
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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
Stable row identifier assigned to the analyzed synthetic construct.
design_label
Author-provided site-mutation label; the workbook's BMHI spelling is retained for the original BMH1 template label.
promoter_template
Promoter template normalized to BMH1 or TDH3.
motif_pattern
Motif-site pattern from the design label; letters denote retained sites and underscores denote mutated sites.
wild_type_construct
Whether the author label identifies the wild-type template construct.
intact_site_count
Number of retained motif sites represented by non-underscore characters in motif_pattern.
mutated_site_count
Number of mutated motif sites represented by underscores in motif_pattern.
promoter_sequence
170-bp user-defined synthetic promoter sequence extracted from the 230-bp library oligonucleotide.
library_barcode
12-bp library barcode embedded in the analyzed 230-bp oligonucleotide.
library_sequence_length_bp
Length of the full library oligonucleotide in base pairs.
binding_replicate_count
Number of CCRA binding replicates reported by the authors for the NBS/SD measurements.
tye7_nbs
Author-provided Tye7p normalized binding score.
tye7_nbs_sd
Author-provided standard deviation of Tye7p normalized binding score.
gcr1_nbs
Author-provided Gcr1p normalized binding score.
gcr1_nbs_sd
Author-provided standard deviation of Gcr1p normalized binding score.
gcr2_nbs
Author-provided Gcr2p normalized binding score.
gcr2_nbs_sd
Author-provided standard deviation of Gcr2p normalized binding score.
reporter_expression_au
Author-provided Sort-Seq YFP reporter expression in arbitrary units.
gcr1_site_score
Author-provided PWM/site score for Gcr1/2p sites retained in the construct.
total_site_score
Author-provided combined site score for the tested TF-collective motif design.
source_sheet
Source worksheet in CCRA_sequences_data.xlsx.
source_geo_samples
GEO sample accession(s) containing the corresponding processed CCRA binding data.
Quality control
The authors designed unique 12-bp library barcodes separated by at least 3 bp and used UMI/coordinate-aware insertion recovery for CCRA binding. Sort-Seq used eight flow-cytometry bins of 100,000 cells and barcode sequencing per bin. Package QC retained 48/48 workbook constructs with 230-bp library sequences, complete 170-bp promoter sequences, and finite binding, standard-deviation, expression, and motif-score values; no rows were removed. The table preserves the authors' expression A.U. scale and per-construct binding SD rather than imposing a new significance cutoff.
Curation notes
This is the genuine MPRA-like reporter-expression component of the study: a plasmid-borne, barcoded promoter array analyzed by fluorescence sorting and sequencing. The paper calls the combined method CCRA; the binding SD values are from four biological/barcode replicates, while the workbook provides one analyzed expression value per construct. Rap1p was not directly measured because it could not be tagged by Sir4p, but Rap1p motif presence contributes to the design/site scores and was evaluated through expression comparisons. The engineered yeast strain yRM1004 has no resolved Cellosaurus accession, so the biosample is explicitly unmapped.