A 100-element synthetic library contained a consensus motif and all single-base substitutions in a matched sequence context, with four barcoded replicates per motif variant. Cbf1p and MAX binding were measured in yeast, and expectation-maximization-corrected scores were used by the authors for binding-energy comparisons.
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
Galactose-induced Ty5 transposition
Each 230-bp library oligonucleotide contains a 170-bp user-defined promoter, a 12-bp library barcode, and constant cloning/amplification sequence. Cbf1p and MAX NBS values are reported before and after the paper's Gaussian-versus-uniform expectation-maximization background correction; the correction was applied for binding-energy landscape generation.
Calling Cards Reporter Arrays (CCRA): a plasmid-borne synthetic promoter library was assayed in engineered Saccharomyces cerevisiae with Cbf1p-Sir4p or MAX-Sir4p-directed Ty5 insertion. The molecular readout is TF-directed insertion occupancy/NBS, not a conventional RNA/DNA reporter ratio.
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 · 27 definitions
element_id
Normalized identifier for the consensus or single-substitution motif variant.
variant_pattern
Author-provided eight-position pattern; underscores mark unchanged consensus positions and the letter marks the substituted base.
variant_class
Consensus or single-base-substitution library design class.
substitution_position_1based
One-based position of the substituted base in the author-provided motif pattern; blank for consensus.
substitution_base
Substituted nucleotide in the motif pattern; blank for consensus.
promoter_sequence
170-bp user-defined synthetic promoter sequence extracted from the 230-bp library oligonucleotide.
library_barcode_replicates
Pipe-separated 12-bp library barcodes for the four replicate oligos.
library_sequence_length_bp
Length of the full library oligonucleotide in base pairs.
replicate_count
Number of source barcode/replicate rows summarized.
cbf1_nbs_mean
Mean Cbf1p normalized binding score across replicates.
cbf1_nbs_sd
Sample standard deviation of Cbf1p normalized binding score.
cbf1_nbs_em_mean
Mean Cbf1p NBS after the expectation-maximization background correction.
cbf1_nbs_em_sd
Sample standard deviation of EM-corrected Cbf1p NBS.
cbf1_unique_insertions_mean
Mean Cbf1p unique insertion count across replicates.
cbf1_unique_insertions_sum
Sum of Cbf1p unique insertion counts across replicates.
cbf1_reads_mean
Mean Cbf1p sequencing read count across replicates.
cbf1_reads_sum
Sum of Cbf1p sequencing reads across replicates.
max_nbs_mean
Mean MAX normalized binding score across replicates.
max_nbs_sd
Sample standard deviation of MAX normalized binding score.
max_nbs_em_mean
Mean MAX NBS after expectation-maximization background correction.
max_nbs_em_sd
Sample standard deviation of EM-corrected MAX NBS.
max_unique_insertions_mean
Mean MAX unique insertion count across replicates.
max_unique_insertions_sum
Sum of MAX unique insertion counts across replicates.
max_reads_mean
Mean MAX sequencing read count across replicates.
max_reads_sum
Sum of MAX sequencing reads across replicates.
source_sheet
Source worksheet in CCRA_sequences_data.xlsx.
source_geo_samples
GEO sample accession(s) containing the corresponding processed binding data.
Quality control
The authors required the expected library/TF barcode structure, classified insertion orientation and position, used UMI/coordinate information to identify independent events, and normalized by full-length library abundance. For affinity analysis they applied an expectation-maximization model to remove estimated uniform background insertions, reported as 0–20% of events in the paper. Package QC retained all 25 motif variants because each had four replicate rows and finite positive binding, insertion, and read metrics.
Curation notes
This table summarizes the author-provided affinity landscape rather than recomputing free-energy differences from the raw insertion-position dictionaries. The library is synthetic and has no genomic coordinates, so reference_genome and region_of_interest are null. The engineered yeast strain yRM1004 has no resolved Cellosaurus accession, so the biosample is explicitly unmapped.