Waern_2013_PMID_23390610.README
Last modified: 2016-07-07

Waern, K. & Snyder, M. (2013) Extensive transcript diversity and novel
upstream open reading frame regulation in yeast. G3 3(2):343-52
PMID: 23390610

Description of data: Differentialy expressed genes under 17 different
growth condtions of the budding yeast genome using RNA-seq and DE-seq
analysis.

Experiment type: RNA-seq
Platform: Illumina GA IIx
Reads: Single End
Strain: BY4741
Genotype: leu2Δ0 ura3Δ0 met15Δ0 his3Δ1
Growth Conditions: 
AlphaFactor
Benomyl
Calcofluor
Congo Red
DNA Damage
Grape Juice (Walgreen's Brand)
Heat Shock
High Calcium
Hydroxyurea
Low Nitrogen
Low Phosphate
Oxidative Stress
Salt
ScGlycerol Media
ScMedia
Sorbitol
Stationary Phase

Data files contained in the compressed file:
Waern_2013_PMID_23390610_track_files.zip

Waern_2013_AlphaFactor.gff3
Waern_2013_Benomyl.gff3
Waern_2013_Calcofluor.gff3
Waern_2013_CongoRed.gff3
Waern_2013_DNADamage.gff3
Waern_2013_GrapeJuice.gff3
Waern_2013_HeatShock.gff3
Waern_2013_HighCalcium.gff3
Waern_2013_Hydroxyurea.gff3
Waern_2013_LowNitrogen.gff3
Waern_2013_LowPhosphate.gff3
Waern_2013_OxidativeStress.gff3
Waern_2013_Salt.gff3
Waern_2013_ScGlycerolMedia.gff3
Waern_2013_ScMedia.gff3
Waern_2013_Sorbitol.gff3
Waern_2013_StationaryPhase.gff3

Waern_2013 GFF3 file version 1.0
Created: 4th May 2013
Last modified: 10th June 2013

GFF3 format description:
Column 1: chromosome name
Column 2: source (First author and publication year, assigned by Waern_2013)
Column 3: feature type (Sequence ontology term assigned by Waern_2013, where applicable)
Column 4: start coordinate of feature (1-based)
Column 5: end coordinate of feature (end inclusive)
Column 6: score where applicable, "." otherwise
Column 7: strand
Column 8: frame where applicable, "." otherwise
Column 9: Feature attributes, detailed below,
  ID: Waern_2013 ID, Unique name for the feature (within this file).
  Name: Gbrowse display name for the feature (assigned by the authors).
  Note: differential expression relative to normal growth conditions 
  symbol: standard gene name                       
 

See additional supplemental files in:
* Waern_2013_PMID_23390610_supplemental_files.zip
* Waern_2013_PMID_23390610_supplemental_files.README