Inter-specific S. cerevisiae × S. uvarum CRE-seq time course
Cis-regulatory variants affect gene expression dynamics in yeastAn integrated CRE-seq library tested 130-bp promoter windows from S. cerevisiae and S. uvarum, including both parental alleles and reciprocal distal/proximal chimeras, in an Oak × S. uvarum diploid. Four random 10-bp barcodes were designed per construct, and barcode RNA/DNA activity was measured over 27 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/DNA27 barcode counts measure library abundance; the processed activity is the per-barcode log2 RNA/DNA ratio after library-size normalization. Allele tokens 3 and 4 are reciprocal distal/proximal chimeras.
Processed data
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Visible columns (55 of 55)
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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 · 55 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: 1 S. cerevisiae, 2 S. uvarum, 3 CU chimera, or 4 UC chimera.
- allele_label
- Human-readable parental or chimera label; the first chimera letter is distal and the second is proximal.
- 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 parental region.
- num_indel_differences
- Number of insertion/deletion differences annotated for the parental region.
- allele_length_1
- Length of the S. cerevisiae allele in the type annotation.
- allele_length_2
- Length of the S. uvarum allele in the type annotation.
- aligned_length
- Alignment length reported in the CRE type annotation.
- n_barcodes_total
- Number of barcodes designed for the construct.
- n_barcodes_qc
- Number of barcode rows retained after the author and region-support QC filters.
- 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 region passed the final parental-replicate support filter; 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_parent_dynamics_significant
- Author significance flag for parental expression dynamics (1=significant, 0=not significant).
- region_parent_levels_significant
- Author significance flag for parental expression levels (1=significant, 0=not significant).
- region_parent_fdr_levels
- Author FDR for the parental CRE expression-level comparison for this region.
- region_parent_fdr_dynamics
- Author FDR for the parental CRE expression-dynamics comparison for this region.
- region_distal_fdr_levels
- Author FDR for the distal chimera genotype expression-level test.
- region_proximal_fdr_levels
- Author FDR for the proximal chimera genotype expression-level test.
- region_distal_fdr_dynamics
- Author FDR for the distal chimera genotype expression-dynamics test.
- region_proximal_fdr_dynamics
- Author FDR for the proximal chimera genotype expression-dynamics test.
- region_cu_vs_cc_fdr_dynamics
- Author FDR for CU versus S. cerevisiae parental dynamics.
- region_cu_vs_uu_fdr_dynamics
- Author FDR for CU versus S. uvarum parental dynamics.
- region_uc_vs_cc_fdr_dynamics
- Author FDR for UC versus S. cerevisiae parental dynamics.
- region_uc_vs_uu_fdr_dynamics
- Author FDR for UC versus S. uvarum parental dynamics.
- region_cu_vs_cc_fdr_levels
- Author FDR for CU versus S. cerevisiae parental levels.
- region_cu_vs_uu_fdr_levels
- Author FDR for CU versus S. uvarum parental levels.
- region_uc_vs_cc_fdr_levels
- Author FDR for UC versus S. cerevisiae parental levels.
- region_uc_vs_uu_fdr_levels
- Author FDR for UC versus S. uvarum parental levels.
- distance_cc_uu
- Author Euclidean expression distance between the two parental genotypes.
- distance_cc_cu
- Author Euclidean expression distance between S. cerevisiae parent and CU chimera.
- distance_uu_cu
- Author Euclidean expression distance between S. uvarum parent and CU chimera.
- distance_cc_uc
- Author Euclidean expression distance between S. cerevisiae parent and UC chimera.
- distance_uu_uc
- Author Euclidean expression distance between S. uvarum parent and UC chimera.
- distance_cu_uc
- Author Euclidean expression distance between the two chimeras.
- timepoint
- CRE-seq RNA sampling label from T1 through T27.
- 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+DNA27 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 27 RNA timepoints, fewer than 100 total DNA1+DNA27 reads, or fewer than 2,700 total RNA reads (100 average reads per timepoint). This retained 5,013 of 7,232 barcode rows. For the final processed table, the author analysis' region-level support filter was also applied: at least two QC-passing barcodes were required for each parental allele, retaining 4,223 barcode rows, 1,383 constructs, and 348 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 labels this library YJF1484 and reports the 5,013-row barcode QC result. The source paper has a typo calling that retained inter-specific count intra-specific in one sentence; this package uses inter.counts.csv and the inter-specific metadata. The final region support filter matches the analysis script's removal of regions with fewer than two parental barcode replicates.