Comment[ArrayExpressAccession]	E-GEOD-32427
Public Release Date	2011-09-30							
Investigation Title	Transcriptome analysis of oocyst, tachyzoite, and bradyzoite development in the type II Toxoplasma gondii strain M4.							
Comment[Submitted Name]	Transcriptome analysis of oocyst, tachyzoite, and bradyzoite development in the type II Toxoplasma gondii strain M4.
Experiment Description	There were three primary objectives to the overall experiment. I.  Describe the transcriptome of the oocyst through its development beginning with the freshly excreted, unsporulated oocyst at “Day 0” to a fully sporulated and mature oocyst at “Day 10” and including a mid-sporulation timepoint at “Day 4”. II. Compare the transcriptomes of in vitro vs. in vivo derived bradyzoites. III. Compare expression data from three life stages (oocyst, bradyzoite and tachyzoite) from the same parasite isolate, M4, which has been been characterized as a Type II strain. Each array represents seperately isolated and processed RNA samples. (Two samples per time point/developmental stage) RNA samples were obtained from: 1.      Oocysts harvested from kitten feces and purified for RNA extraction at Day 0, (not sporulated), Day 4 post-induction of sporulation (mid-sporulation) and Day 10 post-induction of sporulation (fully sporulated).  Oocysts were collected and combined from two kittens that were infected with the same starting material (mouse brains containing bradyzoite cysts of the same parasite strain).  Duplicate samples were obtained from feces collected and purified on separate days. 2.      Bradyzoite cysts harvested from the brains of mice that were infected with oocysts from the same strain (obtained from the oocysts harvested from kittens as described for the oocyst RNA). Mice were treated with 0.44 µg/ml sulfadiazine in their water days 11-21 pi. Mice were sacrificed on day 21 for cyst purification. 3.      In vitro 4 and 8 dpi bradyzoite and 2 dpi tachyzoite samples are from separately infected cultures of human foreskin fibroblasts (HFFs) (replicates were infected on the same day). The parasites used for the initial infections were derived from the same culture. Samples were harvested independently and kept separate for all the subsequent processing and labeling steps.							
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Term Source File	http://www.ebi.ac.uk/efo/efo.owl							
Person Last Name	Buchholz	Fritz	Buchholz	Conrad	Boothroyd	Chen	Durbin-Johnson	Rocke
Person First Name	Kerry	Heather	Kerry	Patricia	John	Xiucui	Blythe	David
Person Mid Initials	R	M	R	A	C			M
Person Email	geo@ncbi.nlm.nih.gov							
Person Affiliation	Stanford University							
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Person Address	Microbiology and Immunology, Stanford University, Fairchild Bld, 299 Campus Drive D305, Stanford, California, USA							
Person Roles	submitter							
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Protocol Name	P-GSE32427-1	P-GSE32427-5	P-GSE32427-4	P-GSE32427-2	P-GSE32427-3	P-GSE32427-7	P-GSE32427-6	P-GSE32427-8
Protocol Description	ID_REF = <br>VALUE = generalized logarithm transformed values	Affymetrix GeneChip Scanner 3000 7G	Affymetrix GeneChip Hybridization Oven 640, Affymetrix GeneChip Fluidics Station 450	TRIzol (Invitrogen) extraction of total RNA	3’ IVT express kit (Affymetrix ) was used to biotin label 250 ng of total RNA.	Data were converted from .cel files and averaged across probes within each probeset using the Bioconductor package affy (version 1.22.1) within the statistical software system R (version 2.10.1), then transformed via a generalized logarithm transformation using the Bioconductor package LMGene  (version 2.4.0).	Software: Affymetrix Genechip Command Console (AGCC)	A one-way analysis of variance (ANOVA) model was fitted to the data one probeset at a time.  For probeset for which the global F test was significant at the 5% level, indicating significant differences between at least two levels of the factor, Tukey HSD post-hoc tests were conducted to test for significant differences among the comparisons of interest.
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Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	nucleic_acid_extraction	labeling	feature_extraction	feature_extraction	feature_extraction
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Experimental Factor Name	DEVELOPMENTAL STAGE							
Experimental Factor Type	developmental stage							
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Comment[SecondaryAccession]	GSE32427							
Comment[GEOLastUpdateDate]	2011-09-30
Comment[AEExperimentType]	transcription profiling by array							
Comment[GEOReleaseDate]	2011-09-29
Comment[ArrayExpressSubmissionDate]	2011-09-26
SDRF File	E-GEOD-32427.sdrf.txt