Comment[ArrayExpressAccession]	E-GEOD-49505
MAGE-TAB Version	1.1						
Public Release Date	2014-05-20
Investigation Title	Gene expression in bovine ovarian follicle theca interna						
Comment[Submitted Name]	Gene expression in bovine ovarian follicle theca interna
Experiment Description	Thecal tissue forms a layer around the follicle just prior to antral stage and grows with the follicle (containing an oocyte) as it matures. The innermost component (theca interna) supplies hormones and other factors necessary to the growth and development of the granulosa and oocyte. Most follicles regress and die (become atretic) at the antral stage, and this process as well as development of the follicle are undoubtedly influenced by the theca. Transcriptional changes in ovarian theca interna at the global level were examined by microarray during atresia and development to improve our understanding of the mechanisms involved. Four groups of bovine ovarian follicles were selected for analysis . Follicle size, type and array number for each group are, small (3-5 mm) healthy rounded (n=5), healthy columnar (n=5), atretic(n=5) and large healthy (>9mm), (n=4). For each group, the RNA from the theca interna of a single follicle was used to hybridise an array.						
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	Hatzirodos	Hatzirodos	Hummitzsch	Irving-Rodgers	Rodgers		
Person First Name	Nicholas	Nicholas	Katja	Helen	Raymond		
Person Mid Initials				F	J		
Person Email	nicholas.hatzirodos@adelaide.edu.au						
Person Affiliation	Adelaide University						
Person Phone	+61 8 8303 3371						
Person Address	Obstetrics and Gynaecology, Adelaide University, Medical School Nth Frome Rd, Adelaide, SA, Australia						
Person Roles	submitter						
Protocol Name	P-GSE49505-1	P-GSE49505-5	P-GSE49505-6	P-GSE49505-2	P-GSE49505-3	P-GSE49505-4	P-GSE49505-7
Protocol Description	The data were analysed in Partek Genomics Suite (v6.5) using RMA (Robust Multi Array Algorithm, Irizarry et al 2003) background corrrection with quantile normalization, mean probe set summarization and adjustment for GC content ID_REF =  VALUE = log base 2 transformed RMA corrected processed data	Biotinylated cRNA was prepared according to the 3' IVT Express labelling kit protocol from 2-5 ug total RNA for the small healthy and large follicles. 250 ng was used for the small atretic follicles(Expression Analysis Technical Manual, 2001, Affymetrix).	Following amplification and fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Bovine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.	Follicles were excised from the ovary, and a piece of wall removed for histological classification. The follicular fluid was released and the granulosa cells scraped from the follicle. The theca interna was then dissected from the follicle wall in cold HankM-bM-^@M-^Ys balanced-salt solution with Mg2+ and Ca2+ and stored at -80M-0C prior to RNA extraction.	Ovarian follicles were obtained from freshly slaughtered non pregnant Bos taurus heifers	Large follicle RNA was extracted using Trizol and purified with Qiagen Rneasy kit columns. Small healthy follicle RNA was extracted using Qiagen Rneasy mini kit columns and small atretic follicle RNA was extracted with RNAqueous Micro kit columns.	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Publication Title	Transcriptome profiling of the theca interna in transition from small to large antral ovarian follicles.						
Publication Author List	Hatzirodos N, Hummitzsch K, Irving-Rodgers HF, Rodgers RJ						
PubMed ID	24830430						
Publication DOI	10.1371/journal.pone.0097489						
Comment[SecondaryAccession]	GSE49505						
Comment[GEOReleaseDate]	2014-05-20						
Comment[ArrayExpressSubmissionDate]	2013-08-02						
Comment[GEOLastUpdateDate]	2014-05-20						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-49505.sdrf.txt