Taf13-depletion sensitivity of yeast UAS–core-promoter combinations
Broad compatibility between yeast UAS elements and core promoters and identification of promoter elements that determine cofactor specificityThe combinatorial episomal reporter library was assayed in the SHY1043 Taf13-degron strain after rapid auxin-mediated Taf13 depletion. This long-format table contains published log2(auxin/no-auxin) reporter fold changes for element–core-promoter pairs, together with their published baseline activity and genomic annotations.
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
500 uM 3-IAA for 30 min versus DMSO vehicle
Episomal yeast reporter plasmids carried genomic UAS/control sequences upstream of the SIT1, KRS1, NOP13, or RPC10 core promoter and an 18 nt randomized barcode. Four biological replicates were performed in two library-transformation batches, with 500 uM 3-indoleacetic acid (auxin) applied for 30 min to the degron strain and DMSO used for the matched no-auxin condition. Nascent 4-thiouracil RNA barcode counts were normalized to DNA plasmid input; the reported depletion endpoint is log2(auxin-treated reporter expression / no-auxin reporter expression).
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 · 32 definitions
- source_table_row
- 1-based row number of the source Table S1 worksheet.
- element_id
- Yeast gene identifier for a UAS or identifier for a genomic control sequence.
- sequence_type
- Source category: UAS, accessible control, or inaccessible control.
- element_sequence
- DNA sequence of the tested UAS or control element as reported in Table S1.
- sequence_length_bp
- Length of element_sequence in base pairs.
- chromosome
- Yeast chromosome for the element or control assignment from the authors' reference tables.
- region_start
- 1-based genomic start coordinate from the authors' reference tables.
- region_end
- 1-based genomic end coordinate from the authors' reference tables.
- strand
- Reported orientation of the tested sequence (+ or −).
- coordinate_source
- Reference file used to add genomic coordinates.
- faire_score
- FAIRE accessibility score for genomic control sequences; blank for UAS rows.
- control_bin
- Authors' genomic control-region bin identifier; blank for UAS rows.
- control_type
- Authors' control type code; blank for UAS rows.
- genomic_tail_dependence
- Endogenous cofactor-tail dependence class associated with the source gene.
- genomic_class
- Endogenous regulatory class associated with the source gene: CR or TFIID.
- genomic_tata_in_promoter
- Endogenous promoter TATA annotation: strong, weak, none, or NA.
- genomic_med8_chec
- Whether the source UAS had detectable genomic Med8 ChEC-seq signal.
- genomic_expression
- Endogenous expression value associated with the source gene in the authors' reference data.
- genomic_med15_depletion_log2fc
- Endogenous genomic log2 fold change after Med15 depletion from the reference dataset.
- genomic_spt7_depletion_log2fc
- Endogenous genomic log2 fold change after Spt7 depletion from the reference dataset.
- genomic_taf13_depletion_log2fc
- Endogenous genomic log2 fold change after Taf13 depletion from the reference dataset.
- core_promoter
- Core-promoter reporter context: SIT1, KRS1, NOP13, or RPC10.
- core_promoter_class
- Regulatory class of the tested core promoter: CR or TFIID.
- core_promoter_tail_dependence
- Tail-dependence annotation of the core promoter: tail-dependent, tail-independent, or NA.
- core_promoter_type
- Core-promoter architecture annotation: TATA-containing or GA-element-containing.
- reporter_expression
- Published normalized no-auxin reporter expression for the element–core-promoter pair, in scaled activity units; not a log2 value.
- paper_qc_pass
- TRUE for rows retained from the paper's final processed Table S1 after endpoint/QC filtering.
- depletion_factor
- The depleted cofactor, Taf13 in this experiment.
- reporter_depletion_log2fc
- Published log2 fold change in reporter transcription for auxin-treated versus no-auxin conditions.
- genomic_depletion_log2fc
- Published endogenous genomic log2 fold change after Taf13 depletion for the source gene, when available.
- reporter_interreplicate_variance
- Published variance of reporter activity across experimental batches/replicates.
- reporter_variance_class
- Published reporter variance class: Low, Intermediate, or High.
Quality control
The study transformed each library at least tenfold above library complexity. Paired-end reads were joined and clustered at 99% similarity for RNA barcode amplicons and 97% similarity for DNA plasmid amplicons; DNA clusters were assigned to UAS/core references by fuzzy sequence matching and RNA barcodes by exact matching. Within each sample, only the most common DNA sequence for each barcode was retained, and barcodes assigned to more than one UAS–core context were removed. Fold changes were calculated only for UAS–core combinations with observations in both auxin and no-auxin conditions. For this package, a row was retained only when the published Taf13 reporter fold-change endpoint and element sequence were present; rows with no valid promoter context were excluded.
Curation notes
The source Table S1 contains 4,464 unique elements. The processed table has 14,709 rows because 49 element rows have no valid Taf13 fold-change context and the remaining elements contribute one to four promoter contexts. Missing contexts reflect the paper's exclusion of combinations with zero observations in either treatment; they are not imputed. The baseline reporter_expression column is included to help distinguish cofactor sensitivity from absolute reporter activity.