Comment[ArrayExpressAccession]	E-GEOD-38570
MAGE-TAB Version	1.1										
Public Release Date	2013-04-15
Investigation Title	Integrated transcriptomic and epigenomic analysis of primary human lung cell differentiation (Rat)										
Comment[Submitted Name]	Integrated transcriptomic and epigenomic analysis of primary human lung cell differentiation (Rat)
Experiment Description	Analysis of gene expression during differentiation of alveolar epithelial type 2 (AT2) cells into AT1 cells. Timepoints taken at Day 0 (AT2 cell), Days 2, 4, and 6 in culture (differentiating) and Day 8 in culture (AT1-like cells). 1ug of RNA was subjected to cRNA conversion using Illumina TotalPrep RNA kit and hybridized to the HT12v4 array Analysis of gene expression during differentiation of alveolar epithelial type 2 (AT2) cells into AT1 cells										
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	Marconett	Marconett	Zhou	Rieger	Selamat	Dubourd	Lynch	Siegmund	Berman	Borok	Laird-Offringa
Person First Name	Crystal	Crystal	Beiyun	Megan	Suhaida	Mickael	Sean	Kimberly	Benjamin	Zea	Ite
Person Mid Initials	N	N			A		K	D	P		A
Person Email	cmarcone@usc.edu										
Person Affiliation	University of Southern California										
Person Phone	323-865-0654										
Person Address	Biochemistry & Molecular Biology, University of Southern California, 1441 Eastlake Ave NOR 6420, Los Angeles, CA, USA										
Person Roles	submitter										
Protocol Name	P-GSE38570-1	P-GSE38570-5	P-GSE38570-6	P-GSE38570-2	P-GSE38570-3	P-GSE38570-4	P-GSE38570-7				
Protocol Description	Using R (version 2.11.1), normalization was performed with VSN using LUMI (Du et al., 2008) to allow for a large number of significantly differentially expressed genes. Statistical analyses were performed using LIMMA (Smyth, 2004). The most variant probes were selected and a linear regression model was fitted over the time-course of differentiation. Technical replicates were removed, and T-tests were performed between Day 0 samples and Day 8 samples. P-values were controlled for false-discovery using the Benjamini-Hochberg (BH) correction (Benjamini & Hochberg, 1995). ID_REF =  VALUE = VSN normalized signal intensity Detection Pval = 	IlluminaTotalPrep RNA kit	Standard Illumina hybridization protocol	Differentiating in culture over time, no extra treatments added.	Rat AT2 cells were isolated as previously described (Zhou et al., 2008; Borok et al., 1998).	RNA was extracted with the Illustra TriplePrep Kit (GE LifeSciences, Piscataway, NJ).	BeadStudio was used to convert images to raw signal data.				
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol				
Experimental Factor Name	TIME	CELL TYPE									
Experimental Factor Type	time	cell type									
Comment[SecondaryAccession]	GSE38570										
Comment[GEOReleaseDate]	2013-04-15										
Comment[ArrayExpressSubmissionDate]	2012-06-07										
Comment[GEOLastUpdateDate]	2013-04-15										
Comment[AEExperimentType]	transcription profiling by array										
Comment[AdditionalFile:Data1]	GSE38570_non-normalized.txt										
SDRF File	E-GEOD-38570.sdrf.txt