Comment[GEAAccession]	E-GEAD-302
MAGE-TAB Version	1.1
Investigation Title	Expression data from mice neonatal testes at days: 7,10,12,14,17
Experiment Description	In an attempt to gain insight into the molecular program of meiosis, we analyzed the transcriptom of the testis during meiosis, using the Affymetrix microarray technology, not restricting ourselves to germ cells or to testis-specific transcripts.Among 6864 sequences that were denoted as ?gpresent?h, only 790 showed an expression level change of twofold or more in any of the five key meiotic stages that were monitored, relative to the geometric average of all stages.
Experimental Design	time series design
Experimental Factor Name	age] Unit[time unit
Experimental Factor Type	age] Unit[time unit
Person Last Name	Don	Ben-Asher
Person First Name	Jeremy	Hiba Waldman
Person Affiliation	The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University	
Person Roles	submitter	submitter
Public Release Date	2019-02-05
PubMed ID	19953644
Protocol Name	P-GEAD-131	P-GEAD-132	P-GEAD-133	P-GEAD-134	P-GEAD-135	P-GEAD-136
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol	normalization data transformation protocol
Protocol Description	Total RNA was isolated from the testes using Tri-reagent solution (Sigma Chemical Co.), according to the manufacturer's protocol.	Total RNA was isolated from the testes using Tri-reagent solution (Sigma Chemical Co.), according to the manufacturer's protocol.	The detailed protocol for preparation and microarray processing is available at Affymetrix http://keck.med.yale.edu/affymetrix/protocols/ (Santa Clara, CA).  Briefly, total RNA was isolated and used as a template for double stranded cDNA synthesis. Double-stranded cDNA was synthesized with a MessageAMP aRNA kit (Ambion) using a T7 oligo(dT) primer. The cDNA was purified with phenol/chloroform, precipitated with ethanol and used as a template for in vitro transcription with biotin labeled nucleotides, biotin-11-CTP and biotin-16-UTP (Enzo Diagnostics, NY, USA).	A total of 15 microg cRNA product in a buffer [40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, 30 mM magnesium acetate] was fragmented at 94 degree C for 35 min, and then added to 300 microl of hybridization mix [10 mg/ml fragmented herring sperm DNA (Promega), 3 nM oligonucleotide B2, hybridization controls (bioB, bioC, bioD, Cre), 50 mg/ml acetylated BSA]. Aliquots of each sample (10 microg cRNA in 200 microl hybridization mix) were hybridized to MGU74v2 affymetrix GeneChip. After hybridization, each array was washed, stained with streptavidin phycoerythrin (Molecular Probes, Oregon, USA), washed again, hybridized with biotin labeled anti streptavidin phycoerythrin antibodies (Vector Laboratories, Burlingame, CA), re-stained with streptavidin phycoerythrin and scanned (Hewlett-Packard, GeneArray scanner G2500A).	Each array was scanned (Hewlett-Packard, GeneArray scanner G2500A).	Signal intensities were normalized using MAS 5.0 software (Affymetrix). Two filtering steps were performed. Approximately 50% of the sequences did not pass the \"present\" expression level threshold, and were discarded. Furthermore, the hybridization control genes that are used to verify that the array yields a sufficient signal, were also disregarded, leaving 6864 \"present\" sequences. In the second filtering step, the expression value of each 'present' sequence, at each post-natal age, was compared to the geometric average of signals obtained for this sequence from all post-natal ages, and only sequences that showed an expression level change of 1 Log2 unit or more, in comparison to the geometric mean were considered for further analysis. This yielded a list of 790 sequences.
SDRF File	E-GEAD-302.sdrf.txt
Comment[Number of channel]	single-channel
Comment[CIBEX Submitter]	Iris Shahar, Assaf Yitzchak, Ramit Mehr, Jeremy Don, Hiba Waldman Ben-Asher
Comment[Array Design REF]	A-AFFY-6
Comment[AEExperimentType]	transcription profiling by array
Comment[SecondaryAccession]	CBX30
Comment[BioProject]	PRJDB7988
Comment[CIBEX Accept Date]	2007-08-02
Comment[CIBEX Public Release Date]	2008-01-07
Comment[Last Update Date]	2019-08-14