--- license: mit language: - en tags: - genomics - yeast - transcription - binding pretty_name: "Harbison, 2004 ChIP-chip" size_categories: - 1M- ChIP-chip data, primarily in standard YPD batch culture, but selected TFs were also tested in specific conditions where they were expected to be active. dataset_type: annotated_features default: true metadata_fields: ["regulator_locus_tag", "regulator_symbol", "condition"] data_files: - split: train path: harbison_2004.parquet dataset_info: features: - name: condition dtype: class_label: names: ["YPD", "SM", "RAPA", "H2O2Hi", "H2O2Lo", "Acid", "Alpha", "BUT14", "BUT90", "Thi-", "GAL", "HEAT", "Pi-", "RAFF"] description: >- Environmental condition of the experiment. Nearly all of the 204 regulators have a YPD condition, and some have others in addition. role: experimental_condition definitions: YPD: description: Standard YPD rich medium; the baseline condition for nearly all 204 regulators. growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.8 od600: 0.8 media: # Harbison et al 2004: 1% yeast extract / 2% peptone / 2% glucose name: YPD carbon_source: - compound: D-glucose concentration_percent: 2 nitrogen_source: - compound: yeast_extract concentration_percent: 1 - compound: peptone concentration_percent: 2 SM: description: Amino acid starvation induced by sulfometuron methyl (SM). growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.6 od600: 0.6 media: # Harbison et al 2004: synthetic complete medium name: synthetic_complete chemical_treatment: compound: sulfometuron_methyl # Harbison et al 2004: 0.2 mg/ml concentration_percent: 0.02 duration_hours: 2 RAPA: description: Rapamycin treatment in YPD to inhibit TORC1 signaling. growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.8 od600: 0.8 media: name: YPD carbon_source: - compound: D-glucose concentration_percent: 2 nitrogen_source: - compound: yeast_extract concentration_percent: 1 - compound: peptone concentration_percent: 2 chemical_treatment: compound: rapamycin # Harbison et al 2004: 100 nM concentration_percent: 9.142e-6 duration_minutes: 20 H2O2Hi: description: High-dose hydrogen peroxide (4 mM) oxidative stress treatment. growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.5 od600: 0.5 media: name: YPD carbon_source: - compound: D-glucose concentration_percent: 2 nitrogen_source: - compound: yeast_extract concentration_percent: 1 - compound: peptone concentration_percent: 2 chemical_treatment: compound: hydrogen_peroxide # Harbison et al 2004: 4 mM concentration_percent: 0.0136 duration_minutes: 30 H2O2Lo: description: Moderate-dose hydrogen peroxide (0.4 mM) oxidative stress treatment. growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.5 od600: 0.5 media: name: YPD carbon_source: - compound: D-glucose concentration_percent: 2 nitrogen_source: - compound: yeast_extract concentration_percent: 1 - compound: peptone concentration_percent: 2 chemical_treatment: compound: hydrogen_peroxide # Harbison et al 2004: 0.4 mM concentration_percent: 0.00136 duration_minutes: 20 Acid: description: Succinic acid treatment in YPD to reach pH 4.0. growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.5 od600: 0.5 media: name: YPD carbon_source: - compound: D-glucose concentration_percent: 2 nitrogen_source: - compound: yeast_extract concentration_percent: 1 - compound: peptone concentration_percent: 2 chemical_treatment: compound: succinic_acid # Harbison et al 2004: 0.05 M to reach pH 4.0 concentration_percent: 0.59 target_pH: 4.0 duration_minutes: 30 Alpha: description: Alpha-factor pheromone treatment to induce the mating response. growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.8 od600: 0.8 media: name: YPD carbon_source: - compound: D-glucose concentration_percent: 2 nitrogen_source: - compound: yeast_extract concentration_percent: 1 - compound: peptone concentration_percent: 2 chemical_treatment: compound: alpha_factor_pheromone # Harbison et al 2004: 5 mg/ml concentration_percent: 0.5 duration_minutes: 30 BUT14: description: YPD with 1% butanol for 14 hours to induce filamentous growth. growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.8 od600: 0.8 media: # Harbison et al 2004: YPD containing 1% butanol name: YPD carbon_source: - compound: D-glucose concentration_percent: 2 nitrogen_source: - compound: yeast_extract concentration_percent: 1 - compound: peptone concentration_percent: 2 additives: - compound: butanol concentration_percent: 1 incubation_duration_hours: 14 BUT90: description: YPD with 1% butanol for 90 minutes to induce filamentous growth. growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.8 od600: 0.8 media: # Harbison et al 2004: YPD containing 1% butanol name: YPD carbon_source: - compound: D-glucose concentration_percent: 2 nitrogen_source: - compound: yeast_extract concentration_percent: 1 - compound: peptone concentration_percent: 2 additives: - compound: butanol concentration_percent: 1 incubation_duration_minutes: 90 "Thi-": description: Synthetic complete medium lacking thiamine (vitamin B1). growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.8 od600: 0.8 media: # Harbison et al 2004: synthetic complete medium lacking thiamin name: synthetic_complete GAL: description: Galactose as sole carbon source in YEP medium. growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.8 od600: 0.8 media: # Harbison et al 2004: YEP medium supplemented with galactose (2%) name: yeast_extract_peptone_galactose carbon_source: - compound: D-galactose concentration_percent: 2 HEAT: description: Temperature shift from 30°C to 37°C for 45 minutes. # Harbison et al 2004: grown at 30°C, shifted to 37°C for 45 min temperature_celsius: 37 growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.5 od600: 0.5 media: # Harbison et al 2004: YPD name: YPD carbon_source: - compound: D-glucose concentration_percent: 2 nitrogen_source: - compound: yeast_extract concentration_percent: 1 - compound: peptone concentration_percent: 2 "Pi-": description: Synthetic complete medium lacking inorganic phosphate. growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.8 od600: 0.8 media: # Harbison et al 2004: synthetic complete medium lacking phosphate name: synthetic_complete RAFF: description: Raffinose as sole carbon source in YEP medium. growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.8 od600: 0.8 media: # Harbison et al 2004: YEP medium supplemented with raffinose (2%) name: yeast_extract_peptone_raffinose carbon_source: - compound: D-raffinose concentration_percent: 2 - name: regulator_locus_tag dtype: string description: Systematic gene name (ORF identifier) of the ChIPd transcription factor role: regulator_identifier - name: regulator_symbol dtype: string description: Standard gene symbol of the ChIPd transcription factor role: regulator_identifier - name: target_locus_tag dtype: string description: Systematic gene name (ORF identifier) of the target gene measured role: target_identifier - name: target_symbol dtype: string description: Standard gene symbol of the target gene measured role: target_identifier - name: effect dtype: float64 description: The chip channel ratio (effect size) role: quantitative_measure - name: pvalue dtype: float64 description: pvalue of the chip channel ratio (effect) role: quantitative_measure --- # Harbison 2004 This Dataset is a parsed version of the data provided by Richard A. Young's lab at [their website](http://younglab.wi.mit.edu/regulatory_code). To cite this data, please use: [Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, et al. 2004. Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99–104.doi:10.1038/nature02800](https://www.nature.com/articles/nature02800)