Cbf1p single-site sensitivity CCRA library
Quantitative analysis of transcription factor binding and expression using calling cards reporter arraysA 40-element synthetic promoter library tested Cbf1p binding at five wild-type promoters or nucleosome-disfavoring sequences and their matched motif-mutant controls. Each of ten constructs was represented by four barcoded library replicates, and TF-directed Ty5 transposition was summarized as a normalized binding score (NBS).
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 library used four unique 12-bp promoter barcodes per construct. The paper normalized independent insertion counts by the abundance of each full-length library element to calculate NBS; the processed table summarizes the four barcode replicates per construct and retains the library sequence and barcode identities.
Calling Cards Reporter Arrays (CCRA): a plasmid-borne synthetic promoter library was assayed in engineered Saccharomyces cerevisiae carrying a Cbf1p-Sir4p fusion and a galactose-inducible Ty5 transposon. TF-directed insertion positions were recovered by paired-end sequencing rather than by a conventional RNA/DNA reporter ratio.
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 · 15 definitions
- element_id
- Normalized identifier for the grouped synthetic promoter construct.
- construct_label
- Author-provided construct label after removing the Rep1–Rep4 prefix.
- motif_status
- Whether the Cbf1p recognition site is present or absent according to the construct label.
- library_sequence
- The author-provided 200-bp library oligonucleotide sequence.
- library_sequence_length_bp
- Length of the library oligonucleotide in base pairs.
- library_barcode_replicates
- Pipe-separated 12-bp barcodes representing the four replicate library elements.
- replicate_count
- Number of source barcode/replicate rows summarized.
- nbs_mean
- Mean normalized binding score across replicate library elements.
- nbs_sd
- Sample standard deviation of normalized binding score across replicate library elements.
- unique_insertions_mean
- Mean number of unique Ty5 insertion events across replicate library elements.
- unique_insertions_sum
- Sum of unique Ty5 insertion events across replicate library elements.
- reads_mean
- Mean sequencing read count across replicate library elements.
- reads_sum
- Sum of sequencing reads across replicate library elements.
- 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 filtered reads for the expected library and TF barcodes, classified Ty5 insertions by orientation and position, used UMI/coordinate information to identify independent events, and normalized by full-length library abundance. Package QC retained constructs with at least two replicate rows, finite NBS/insertion/read values, and non-empty library sequences; all 10 constructs (40 source replicate rows) passed, including valid zero-binding negative-control measurements.
Curation notes
This is a CCRA binding subexperiment from the paper's hybrid reporter-array method; no element-level reporter-expression values were released for this library. The workbook labels five site-present/site-absent pairs and four replicate rows per construct; zero NBS is retained as a valid negative-control result rather than treated as missing data. The engineered yeast strain yRM1004 has no resolved Cellosaurus accession, so the biosample is explicitly unmapped.