Comment[ArrayExpressAccession]	E-GEOD-57031
MAGE-TAB Version	1.1							
Public Release Date	2014-04-24
Investigation Title	Transcriptional regulation by Pho23 modulates the frequency of autophagosome formation.							
Comment[Submitted Name]	Transcriptional regulation by Pho23 modulates the frequency of autophagosome formation.
Experiment Description	Autophagy as a conserved degradation and recycling machinery is important in normal development and physiology, and defects in this process are linked to many kinds of disease. Because too much or too little autophagy can be detrimental, the process must be tightly regulated both temporally and in magnitude. The transcriptional induction and repression of the autophagy-related (ATG) genes is one crucial aspect of this regulation, but the transcriptional regulators that modulate autophagy are not well characterized. In this study, we identified Pho23 as a master transcriptional repressor for autophagy, with transcriptome profiling revealing that ATG9 is one of the key target genes. Physiological studies with a PHO23 null mutant, or with strains expressing modulated levels of Atg9, demonstrate a critical role of this protein as a regulator of autophagosome formation frequency; Atg9 protein levels correlate with the number of autophagosomes generated upon autophagy induction, and the level of autophagy activity. WT yeast and pho23 deletion mutants were grown under nutrient rich or nitrogen starvation conditions; gene expression was quantified across these 4 samples.							
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl						
Person Last Name	Freeberg	Jin	He	Backues	Freeberg	Liu	Kim	Klionsky
Person First Name	Mallory	Meiyan	Ding	Steven	Mallory	Xu	John	Daniel
Person Mid Initials	Ann			K	A		K	J
Person Email	mafree@umich.edu							
Person Affiliation	University of Michigan							
Person Address	Department of Computational Medicine and Bioinformatics, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, USA							
Person Roles	submitter							
Protocol Name	P-GSE57031-3	P-GSE57031-2	P-GSE57031-1					
Protocol Description	Base calling was performed according to Illumina's protocols using RTA v1.13.48.0 and CASAVA v1.8.2. Low-quality reads were removed if they met any of the following criteria: <18 nt, only homopolymer As, missing 3’ adapter, 5’-3’ adapter ligation products, 5’-5’ adapter ligation products, low quality (more than 4 bases with quality scores below 10 or more than 6 bases with a quality score below 13). High-quality reads were aligned to S. cerevisiae transcriptome taken from the genome version sacCer3 using Bowtie2 v2.1.0 with the parameters -f --local -k 500 -p 2. Read counts in each library were normalized to the total number of mapped reads in millions (RPM). Reads mapping uniquely to the transcriptome with zero mismatches were were used to calculate RPM per kilobase of transcript (RPKM) for each gene. Genome_build: SGD/sacCer3 (April 2011) from S288C strain Supplementary_files_format_and_content: Normalized transcript abundance (RPKM) is presented for each transcript in each RNA-seq library.	Total RNAs were extracted using the Master-Pure yeast RNA purification Kit from Epicentre Biotechnologies. cDNA library preparation was performed by the DNA sequencing core at the University of Michigan.	Yeast cells were grown in rich medium (YPD) to mid-log phase growth. Yeast cells subjected to starvation conditions were then shifted to SD-N for 2 hours.					
Protocol Type	normalization data transformation protocol	nucleic acid library construction protocol	growth protocol					
Experimental Factor Name	BARCODE	GENOTYPE	CONDITION					
Experimental Factor Type	barcode	genotype	condition					
Comment[SecondaryAccession]	GSE57031							
Comment[GEOReleaseDate]	2014-04-24							
Comment[ArrayExpressSubmissionDate]	2014-04-23							
Comment[GEOLastUpdateDate]	2014-04-24							
Comment[AEExperimentType]	RNA-seq of coding RNA							
Comment[AdditionalFile:Data1]	GSE57031_Gene_RPKM.txt							
Comment[SecondaryAccession]	SRP041400							
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR1259524-SRR1259527							
SDRF File	E-GEOD-57031.sdrf.txt