metadata
license: mit
language:
- en
tags:
- genomics
- yeast
- transcription
- binding
pretty_name: Harbison, 2004 ChIP-chip
size_categories:
- 1M<n<10M
strain_information:
background: W303
base_strain: Z1256
experimental_conditions:
temperature_celsius: 30
doi: https://doi.org/10.1038/nature02800
citation: >-
Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, et al. 2004.
Transcriptional regulatory code of a eukaryotic genome. Nature.
configs:
- config_name: harbison_2004
description: >-
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:
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
SM:
description: Amino acid starvation induced by sulfometuron methyl (SM).
growth_phase_at_harvest:
od600: 0.6
media:
name: synthetic_complete
chemical_treatment:
compound: sulfometuron_methyl
concentration_percent: 0.02
duration_hours: 2
RAPA:
description: Rapamycin treatment in YPD to inhibit TORC1 signaling.
growth_phase_at_harvest:
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
concentration_percent: 0.000009142
duration_minutes: 20
H2O2Hi:
description: High-dose hydrogen peroxide (4 mM) oxidative stress treatment.
growth_phase_at_harvest:
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
concentration_percent: 0.0136
duration_minutes: 30
H2O2Lo:
description: >-
Moderate-dose hydrogen peroxide (0.4 mM) oxidative stress
treatment.
growth_phase_at_harvest:
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
concentration_percent: 0.00136
duration_minutes: 20
Acid:
description: Succinic acid treatment in YPD to reach pH 4.0.
growth_phase_at_harvest:
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
concentration_percent: 0.59
target_pH: 4
duration_minutes: 30
Alpha:
description: Alpha-factor pheromone treatment to induce the mating response.
growth_phase_at_harvest:
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
concentration_percent: 0.5
duration_minutes: 30
BUT14:
description: YPD with 1% butanol for 14 hours to induce filamentous growth.
growth_phase_at_harvest:
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
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:
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
additives:
- compound: butanol
concentration_percent: 1
incubation_duration_minutes: 90
Thi-:
description: Synthetic complete medium lacking thiamine (vitamin B1).
growth_phase_at_harvest:
od600: 0.8
media:
name: synthetic_complete
GAL:
description: Galactose as sole carbon source in YEP medium.
growth_phase_at_harvest:
od600: 0.8
media:
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.
temperature_celsius: 37
growth_phase_at_harvest:
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
Pi-:
description: Synthetic complete medium lacking inorganic phosphate.
growth_phase_at_harvest:
od600: 0.8
media:
name: synthetic_complete
RAFF:
description: Raffinose as sole carbon source in YEP medium.
growth_phase_at_harvest:
od600: 0.8
media:
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. DOI and citation are in the dataset card above, or see the ArrayExpress entry
Accessing Data
The examples below require
labretriever
(pip install labretriever) and/or the
HuggingFace Hub client
(pip install huggingface_hub).
Accessing Data with labretriever
This repository is part of a collection configured as a unified database using labretriever.VirtualDB. Download the collection config and use it to query the data directly in Python, or with an AI assistant using the labretriever plugin.
from labretriever.virtual_db import VirtualDB
from labretriever.datacard import DataCard
# Citation and metadata
card = DataCard("BrentLab/harbison_2004")
info = card.info()
print(info["doi"])
print(info["citation"])
# path to the downloaded brentlab_yeast_collection.yaml
vdb = VirtualDB("/path/to/brentlab_yeast_collection.yaml")
print(vdb.get_dataset_description("harbison"))
vdb.query("SELECT * FROM harbison LIMIT 5")
Direct parquet access
The repository contains more data than what is exposed through the collection
configuration. Use DataCard.info() to inspect available files, then download
and query with DuckDB.
Most files in this repository are single parquet files and can be read directly:
from huggingface_hub import snapshot_download
import duckdb
repo_path = snapshot_download(
repo_id="BrentLab/harbison_2004",
repo_type="dataset",
allow_patterns="harbison_2004.parquet",
)
conn = duckdb.connect()
# returns a pandas DataFrame with the first 5 rows
conn.execute(
"SELECT * FROM read_parquet(?) LIMIT 5",
[f"{repo_path}/harbison_2004.parquet"],
).df()
Accessing using R
Clone the repository and read parquet files directly with arrow:
# install.packages("arrow")
arrow::read_parquet("harbison_2004.parquet")