Cbf1p homotypic cooperativity spacing CCRA library
Quantitative analysis of transcription factor binding and expression using calling cards reporter arraysA 68-element synthetic promoter library varied the spacing between two Cbf1p consensus motifs from 9 to 41 bp in 2-bp increments. Each of the 17 spacing designs was represented by four barcoded replicates and assayed for Cbf1p-directed Ty5 insertion occupancy.
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
Galactose-induced Ty5 transposition
The variable 170-bp promoter sequences contain two Cbf1p sites at the indicated core-to-core spacing. Four independent barcode/replicate library elements were summarized for each spacing, using the paper's NBS normalization by full-length library abundance.
Calling Cards Reporter Arrays (CCRA): a plasmid-borne synthetic promoter library was assayed in engineered Saccharomyces cerevisiae carrying Cbf1p-Sir4p and a galactose-inducible Ty5 transposon. The molecular readout is normalized TF-directed insertion occupancy rather than 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 · 15 definitions
- element_id
- Normalized identifier for the motif-spacing construct.
- spacing_description
- Author-provided description of the Cbf1p motif spacing.
- spacing_between_core_motifs_bp
- Distance in base pairs between the cores of the two Cbf1p motifs.
- promoter_sequence
- 170-bp user-defined synthetic promoter sequence extracted from the 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.
- nbs_mean
- Mean Cbf1p normalized binding score across replicates.
- nbs_sd
- Sample standard deviation of Cbf1p normalized binding score.
- unique_insertions_mean
- Mean number of unique Cbf1p-directed Ty5 insertion events across replicates.
- unique_insertions_sum
- Sum of unique Cbf1p-directed insertion events across replicates.
- reads_mean
- Mean sequencing read count across replicates.
- reads_sum
- Sum of sequencing reads across replicates.
- source_sheet
- Source worksheet in CCRA_sequences_data.xlsx.
- source_geo_samples
- GEO sample accession containing the corresponding processed binding data.
Quality control
Reads were filtered for expected library and TF barcodes, insertion orientation/position was classified, UMI/coordinate information was used to identify independent events, and counts were normalized by library-element abundance. Package QC retained all 17 spacing designs because each had four replicate rows, finite NBS/insertion/read values, and the expected 230-bp library sequence; no rows were removed.
Curation notes
This is the synthetic spacing/cooperativity binding subexperiment. Because the constructs are synthetic and not genomic intervals, reference_genome and region_of_interest are null. The engineered yeast strain yRM1004 has no resolved Cellosaurus accession, so the biosample is explicitly unmapped.