Intra-specific Oak × ChII CRE-seq time course
Cis-regulatory variants affect gene expression dynamics in yeastAn integrated CRE-seq library tested 130-bp promoter windows, parental alleles, and single-variant substitutions from the Oak (YJF153) and China II (SX6) Saccharomyces cerevisiae strains in an Oak × ChII diploid. Four random 10-bp barcodes were designed per construct, and barcode RNA/DNA activity was measured over 19 diauxic-shift timepoints.
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
CRE-seq reporter assay: pooled 200-bp synthetic oligos were cloned into pIM202, YFP was placed between the cis-regulatory element and barcode, and the reporter library was integrated at the URA3 locus in yeast. RNA barcode counts measure reporter expression and combined DNA1/DNA19 barcode counts measure library abundance; the processed activity is the per-barcode log2 RNA/DNA ratio after library-size normalization.
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 · 49 definitions
- element_id
- Unique CRE construct identifier without the barcode sequence.
- gene_id
- Systematic S. cerevisiae gene identifier targeted by the promoter region.
- region_id
- Gene and promoter-window identifier in the form gene:region.
- region
- Promoter window index; 0 is proximal to the TSS and 4 is most distal.
- allele
- Library allele token: 0 shared sequence, 1 Oak, 2 ChII, vaN Oak variant in ChII background, or vbN ChII variant in Oak background.
- allele_label
- Human-readable allele or substitution label.
- construct_type
- Functional class of the tested construct.
- promoter_sequence
- Synthetic cis-regulatory sequence used in the reporter construct.
- promoter_sequence_length
- Length in bases of promoter_sequence.
- oligo_length
- Designed synthetic oligo length in bases.
- num_snp_differences
- Number of SNP differences annotated for the construct or parental region.
- num_indel_differences
- Number of insertion/deletion differences annotated for the construct or parental region.
- allele_length_1
- Length of the first parental allele in the type annotation.
- allele_length_2
- Length of the second parental allele in the type annotation.
- aligned_length
- Alignment length reported in the CRE type annotation, when available.
- n_barcodes_total
- Number of barcodes designed for the construct.
- n_barcodes_qc
- Number of barcode rows retained after the author QC filter.
- qc_pass_rate
- n_barcodes_qc divided by n_barcodes_total.
- qc_barcodes
- Semicolon-separated barcode sequences retained after QC.
- region_qc_retained
- Indicates that the construct belongs to the processed QC-retained set; 1 means yes.
- region_correlated_with_rnaseq
- Author annotation indicating whether the promoter region correlated with endogenous RNA-seq expression (1=yes, 0=no).
- region_fdr_levels
- Author FDR for the parental CRE expression-level comparison for this region.
- region_fdr_dynamics
- Author FDR for the parental CRE expression-dynamics comparison for this region.
- region_parents_dynamics
- Author significance flag for parental expression dynamics (1=significant, 0=not significant).
- region_parents_levels
- Author significance flag for parental expression levels (1=significant, 0=not significant).
- published_comparison
- Matched comparison in intra.stats.csv: 2 for parental alleles or vN for single-variant tests.
- published_comparison_type
- Whether the matched published comparison is parental or single-variant.
- published_n_snps
- Number of SNPs reported for the matched published comparison.
- published_n_indels
- Number of InDels reported for the matched published comparison.
- published_comparison_fdr_levels
- Author FDR for expression levels in the matched comparison.
- published_comparison_fdr_dynamics
- Author FDR for expression dynamics in the matched comparison.
- published_comparison_parents_dynamics
- Author parental-dynamics flag in the matched statistics row.
- published_comparison_parents_levels
- Author parental-levels flag in the matched statistics row.
- published_rnaseq_dynamics_significant
- Author endogenous RNA-seq dynamics significance flag.
- published_rnaseq_levels_significant
- Author endogenous RNA-seq levels significance flag.
- published_level_variant_flag
- Author flag that the tested comparison identified a level-affecting variant.
- published_dynamics_variant_flag
- Author flag that the tested comparison identified a dynamics-affecting variant.
- timepoint
- CRE-seq RNA sampling label from T1 through T19.
- time_hours
- Sampling time in hours during the diauxic shift, from the authors' CRE_analysis.R time vector.
- n_barcodes_with_activity
- Number of retained barcodes with nonzero RNA and positive DNA used for the activity summary at this timepoint.
- mean_rna_count
- Mean raw RNA barcode count across retained barcodes for this construct and timepoint.
- mean_dna_count
- Mean combined DNA1+DNA19 barcode count across retained barcodes for this construct.
- mean_rna_cpm
- Mean RNA count after per-timepoint library-size normalization to counts per million.
- mean_dna_cpm
- Mean combined DNA count after library-size normalization to counts per million.
- mean_log2_activity
- Mean barcode-level log2[(RNA CPM)/(combined DNA CPM)] at this timepoint; zero-RNA barcodes are omitted.
- sem_log2_activity
- Standard error of the barcode-level log2 activity mean at this timepoint.
- mean_activity_over_time
- Mean of mean_log2_activity across timepoints with nonmissing activity for this construct.
- sd_activity_over_time
- Standard deviation of mean_log2_activity across informative timepoints for this construct.
- n_timepoints_with_activity
- Number of timepoints with a nonmissing construct activity summary.
Quality control
Author-described QC was applied to the raw barcode counts: perfect matches to library barcodes were retained, technical replicate libraries were combined, and a barcode was removed if it had zero RNA reads in more than one-third of the 19 RNA timepoints, fewer than 100 total DNA1+DNA19 reads, or fewer than 1,900 total RNA reads (100 average reads per timepoint). This retained 6,820 of 7,268 barcode rows, corresponding to 1,816 constructs across 334 promoter regions. Zero RNA timepoints are omitted from activity means and standard errors. The processed activity uses transparent library-size-normalized CPM RNA divided by combined-DNA CPM; the original count files and author statistics are included in raw_data.
Curation notes
The paper calls this the YJF1455 intra-specific library. The 0 allele token denotes a single shared sequence for regions where the Oak and ChII windows are identical; those constructs have no parental comparison row in intra.stats.csv. vaN means Oak sequence substituted into a ChII background, while vbN means the reciprocal ChII substitution.