Genome-integrated CRE-seq synthetic promoter library
Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variantsA genome-integrated CRE-seq library in Saccharomyces cerevisiae BY4742 tested randomly ligated combinations of 12 Mig1, Reb1, Rap1, and Gcr1 TFBS variants upstream of a TSA1-YFP reporter with 15-nt 3′-UTR barcodes. The processed table aggregates the author-provided barcode-level normalized gDNA/cDNA measurements to one row per synthetic promoter label.
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
Basal / Untreated
CRE-seq was adapted for chromosomal integration in S. cerevisiae: synthetic TFBS oligos were randomly ligated into a promoter library, cloned into pIM202, placed upstream of a TSA1 basal promoter driving YFP, and integrated at the TRP1 locus. Each construct carried a transcribed 15-nt barcode in the YFP 3′ UTR; RNA/cDNA barcode abundance was normalized to gDNA barcode abundance, with an integration-control gDNA PCR used to retain correctly integrated constructs. The library was grown in synthetic complete medium lacking uracil with 2% glucose at 30°C for 5 h before gDNA and RNA collection.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (29 of 29)
| Row | |||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | |||||||||||||||||||||||||||||
| 2 | |||||||||||||||||||||||||||||
| 3 | |||||||||||||||||||||||||||||
| 4 | |||||||||||||||||||||||||||||
| 5 | |||||||||||||||||||||||||||||
| 6 | |||||||||||||||||||||||||||||
| 7 | |||||||||||||||||||||||||||||
| 8 | |||||||||||||||||||||||||||||
| 9 | |||||||||||||||||||||||||||||
| 10 | |||||||||||||||||||||||||||||
| 11 | |||||||||||||||||||||||||||||
| 12 | |||||||||||||||||||||||||||||
| 13 | |||||||||||||||||||||||||||||
| 14 | |||||||||||||||||||||||||||||
| 15 | |||||||||||||||||||||||||||||
| 16 | |||||||||||||||||||||||||||||
| 17 | |||||||||||||||||||||||||||||
| 18 | |||||||||||||||||||||||||||||
| 19 | |||||||||||||||||||||||||||||
| 20 | |||||||||||||||||||||||||||||
| 21 | |||||||||||||||||||||||||||||
| 22 | |||||||||||||||||||||||||||||
| 23 | |||||||||||||||||||||||||||||
| 24 | |||||||||||||||||||||||||||||
| 25 | |||||||||||||||||||||||||||||
| 26 | |||||||||||||||||||||||||||||
| 27 | |||||||||||||||||||||||||||||
| 28 | |||||||||||||||||||||||||||||
| 29 | |||||||||||||||||||||||||||||
| 30 | |||||||||||||||||||||||||||||
| 31 | |||||||||||||||||||||||||||||
| 32 | |||||||||||||||||||||||||||||
| 33 | |||||||||||||||||||||||||||||
| 34 | |||||||||||||||||||||||||||||
| 35 | |||||||||||||||||||||||||||||
| 36 | |||||||||||||||||||||||||||||
| 37 | |||||||||||||||||||||||||||||
| 38 | |||||||||||||||||||||||||||||
| 39 | |||||||||||||||||||||||||||||
| 40 | |||||||||||||||||||||||||||||
| 41 | |||||||||||||||||||||||||||||
| 42 | |||||||||||||||||||||||||||||
| 43 | |||||||||||||||||||||||||||||
| 44 | |||||||||||||||||||||||||||||
| 45 | |||||||||||||||||||||||||||||
| 46 | |||||||||||||||||||||||||||||
| 47 | |||||||||||||||||||||||||||||
| 48 | |||||||||||||||||||||||||||||
| 49 | |||||||||||||||||||||||||||||
| 50 |
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 29 definitions
- element_id
- Stable package identifier for the synthetic promoter label.
- promoter_label
- PROM label from the source barcode table, encoding the ordered TFBS-token architecture.
- known_site_tokens
- Semicolon-separated M/R/P/G TFBS tokens resolved from Table 1; case and variant number are preserved.
- unresolved_tokens
- Semicolon-separated promoter tokens not defined by the source comments/Table 1, currently B/b tokens.
- oriented_site_sequences
- Semicolon-separated token:sequence annotations; known lower-case reverse-orientation sites are reverse-complemented, and unresolved tokens are marked UNMAPPED.
- site_count_total
- Total number of parsed site tokens, including unresolved tokens.
- known_tfbs_site_count
- Number of parsed TFBS tokens resolved to Mig1, Reb1, Rap1, or Gcr1.
- unresolved_site_count
- Number of parsed unresolved B/b or other non-reference tokens.
- mig1_site_count
- Count of Mig1 variant tokens (M/m).
- reb1_site_count
- Count of Reb1 variant tokens (R/r).
- rap1_site_count
- Count of Rap1 variant tokens (P/p).
- gcr1_site_count
- Count of Gcr1 variant tokens (G/g).
- known_forward_site_count
- Count of resolved TFBS tokens in forward orientation (upper-case).
- known_reverse_site_count
- Count of resolved TFBS tokens in reverse orientation (lower-case).
- n_barcodes_source
- Number of barcode records for the PROM label in the supplied source file before package QC.
- n_barcodes_qc
- Number of unique-barcode records retained after package QC.
- barcode_ids_qc
- Semicolon-separated retained barcode sequences supporting the promoter row.
- gDNA_expr_norm_median
- Median source-normalized gDNA barcode abundance for the promoter’s retained barcodes.
- cDNA_expr_norm_median
- Median source-normalized cDNA barcode abundance for the promoter’s retained barcodes.
- gDNA_integration_norm_median
- Median source-normalized integration-control gDNA abundance for the promoter’s retained barcodes.
- gDNA_expr_norm_min
- Minimum retained-barcode source-normalized gDNA abundance.
- gDNA_integration_norm_min
- Minimum retained-barcode source-normalized integration-control abundance.
- barcode_expr_ratio_median
- Median barcode-level EXPR value, representing the source cDNA/gDNA expression ratio.
- activity_log2_median
- Log2 of the promoter-level median barcode expression ratio; primary processed activity score.
- activity_log2_mean
- Mean of log2 barcode expression ratios across retained barcodes.
- activity_log2_sd
- Sample standard deviation of log2 barcode expression ratios across retained barcodes.
- barcode_expr_ratio_q25
- 25th percentile of retained-barcode expression ratios.
- barcode_expr_ratio_q75
- 75th percentile of retained-barcode expression ratios.
- qc_pass
- Boolean flag; all rows in this filtered table passed package QC.
Quality control
The source study filtered CRE/BC assignments using mapping-read support, a ≥90% dominant CRE assignment when a barcode mapped ambiguously, sequencing-error-like barcode removal, correct-integration control, >25 gDNA reads, and at least one cDNA read before calculating barcode expression. For this package, the supplied normalized table was additionally filtered to valid promoter-token architecture, exactly 15-base A/C/G/T barcodes, finite positive normalized measurements, and a consistent cDNA/gDNA ratio; both records for the single duplicated barcode sequence CGGCACGCGACCGTC were removed to preserve unique barcode identifiers. Two malformed PROM records and 99 non-15-base barcode records were excluded. The final table retains 6,805 barcode observations across 2,436 promoter labels and does not impose a minimum barcode multiplicity because the source study includes one-barcode promoters; the paper’s thermodynamic-model outlier filter cannot be reproduced from this released file.
Curation notes
The source article describes 7,289 barcodes and 2,534 final CREs, while its Methods also mention an intermediate 2,633 mapped CREs; the mirrored Supplemental Data 2 available for packaging contains 6,908 records and 2,467 PROM labels, and the table follows the supplied file. The article’s model-based exclusion of approximately 100 outlier promoters is not reproducible without its hidden model inputs, so promoter rows with at least one package-QC-passing barcode are retained. B/b tokens occur in the source PROM labels but are not defined in the source comments or Table 1; they are preserved as unresolved rather than assigned a TF. The packaged experiment represents the main integrated synthetic-promoter barcode assay; the paper’s flow-cytometry validation is not a separate MPRA table.