Full-length Oak/ChII promoter CRE-seq validation
Cis-regulatory variants affect gene expression dynamics in yeastFull-length promoters from ALD5, GND2, and PHO3 in Oak and ChII backgrounds were barcoded and integrated at URA3 in the Oak × ChII diploid. The supplied full-length count/activity file was summarized by gene, allele, and measured timepoint.
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
Diauxic-shift time course in YPD at 30°C; no exogenous treatment
Full-length promoter CRE-seq extension using the pIM202/YFP/barcode reporter integrated at the URA3 locus. Oak and ChII full-length promoter constructs were assayed by barcode RNA/DNA ratios; the supplied file contains the source exp value, RNA count, and DNA count but does not retain barcode sequence identifiers.
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 · 19 definitions
- element_id
- Unique full-length promoter construct identifier.
- gene_name
- Common gene name: ALD5, GND2, or PHO3.
- systematic_gene_id
- Systematic S. cerevisiae gene identifier corresponding to gene_name.
- allele
- Promoter allele, Oak or ChII.
- allele_label
- Human-readable promoter allele label.
- construct_type
- Full-length promoter reporter construct.
- promoter_scope
- Promoter scope represented by the construct; full_length.
- n_barcodes_total
- Number of barcodes designed per full-length promoter construct.
- n_observations
- Number of source records observed in this gene-allele-timepoint cell.
- qc_pass_rate
- n_observations divided by four designed barcode observations; source records lack barcode IDs.
- timepoint
- Sequential measured timepoint label assigned after sorting the source time values.
- time_hours
- Measured sampling time in hours from the source file.
- mean_rna_count
- Mean supplied RNA barcode count for this gene, allele, and timepoint.
- mean_dna_count
- Mean supplied DNA barcode count for this gene, allele, and timepoint.
- mean_log2_activity
- Mean supplied exp value, representing the source barcode RNA/DNA activity on a log2 scale.
- sem_log2_activity
- Standard error of the supplied exp values within this gene-allele-timepoint cell.
- mean_activity_over_time
- Mean of the timepoint mean_log2_activity values for this promoter allele.
- sd_activity_over_time
- Standard deviation of timepoint mean_log2_activity values for this promoter allele.
- n_timepoints_with_activity
- Number of measured timepoints contributing to the promoter-allele activity summary.
Quality control
The supplied full.length.counts.csv contains 360 positive RNA/DNA observations for six promoter-allele constructs across 20 measured timepoints; no zero-count records were present and no additional author filter was documented for this validation file. All positive observations were retained and aggregated by gene, allele, and timepoint. Four barcodes were designed per construct, but the source file does not identify individual barcode sequences and contains 2–4 observed records per gene-allele-timepoint cell.
Curation notes
The full-length promoter records are a validation extension of the short CRE-seq assay, not a separate genomic region screen. The source table contains no barcode sequence or construct sequence columns, so sequence-level details remain in the short-library raw files and the full-length table is intentionally an aggregate summary.