Tye7p/Gcr1p/Cbf1p promoter reprogramming CCRA library
Quantitative analysis of transcription factor binding and expression using calling cards reporter arraysA 16-element library compared native OYE3_DAP1 and RPL1_RHO3 Cbf1p-target promoter sequences with versions in which Cbf1p motifs were removed and TDH3-derived Gcr1p/Gcr2p and Rap1p sites were added. Four barcoded replicates per construct were assayed for Tye7p, Gcr1p, and Cbf1p binding.
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
Tye7p, Gcr1p, and Cbf1p were measured on the same 230-bp library designs. The table summarizes four barcode/replicate rows for each of four constructs and exposes the 170-bp user-defined promoter sequence separately from the constant library sequence.
Calling Cards Reporter Arrays (CCRA): promoter variants were cloned into the pRM1806 reporter-library plasmid and assayed in engineered Saccharomyces cerevisiae with TF-Sir4p fusions and a galactose-inducible Ty5 transposon. The reported binding readout is normalized insertion occupancy/NBS.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (16 of 16)
| Row | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ||||||||||||||||
| 2 | ||||||||||||||||
| 3 | ||||||||||||||||
| 4 |
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 16 definitions
- element_id
- Normalized identifier for the promoter construct.
- design_label
- Author-provided construct label.
- promoter_template
- Native promoter template used as the starting sequence: OYE3_DAP1 or RPL1_RHO3.
- construct_status
- Native construct or construct reprogrammed with TDH3-derived 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.
- binding_replicate_count
- Number of source barcode/replicate rows summarized.
- tye7_nbs_mean
- Mean Tye7p normalized binding score across replicates.
- tye7_nbs_sd
- Sample standard deviation of Tye7p normalized binding score.
- gcr1_nbs_mean
- Mean Gcr1p normalized binding score across replicates.
- gcr1_nbs_sd
- Sample standard deviation of Gcr1p normalized binding score.
- cbf1_nbs_mean
- Mean Cbf1p normalized binding score across replicates.
- cbf1_nbs_sd
- Sample standard deviation of Cbf1p normalized binding score.
- 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 expected library and TF barcodes, classified Ty5 insertion orientation/position, deduplicated independent events using UMI/coordinate information, and normalized by full-length library abundance. Package QC retained all four constructs because each had four replicate rows, finite Tye7p/Gcr1p/Cbf1p NBS values, and a complete 230-bp library sequence.
Curation notes
The reprogramming designs are synthetic promoter constructs, not genomic coordinates. Rap1p was part of the motif design but was not directly assayed in the paper because it could not be tagged with Sir4p. The engineered yeast strain yRM1004 has no resolved Cellosaurus accession, so the biosample is explicitly unmapped.