Comment[ArrayExpressAccession]	E-GEOD-57109
MAGE-TAB Version	1.1				
Public Release Date	2014-07-29
Investigation Title	A new dataset of spermatogenic vs oogenic transcriptomes in the nematode C. elegans				
Comment[Submitted Name]	A new dataset of spermatogenic vs oogenic transcriptomes in the nematode C. elegans
Experiment Description	The nematode Caenorhabditis elegans is an important model for studies of germ cell biology, including specification as sperm or oocyte, the meiotic cell cycle and gamete differentiation.  Fundamental to those studies is a genome-level knowledge of the germline transcriptome.  Here we use RNA-Seq to identify genes expressed in isolated XX gonads, which are roughly 95% germline and 5% somatic gonadal tissue.  We generate data from mutants making either sperm [fem-3(q96)] or oocytes (fog-2), both grown at 22M-BM-0C.  Our dataset identifies a total of 10,754 mRNAs in the polyadenylated transcriptome of XX gonads, with 1,723 enriched in spermatogenic gonads, 2,869 enriched in oogenic gonads and the remaining 6,274 not enriched in either.  These spermatogenic, oogenic and gender-neutral gene datasets compare well with those of earlier studies, but double the number of genes identified.  We also query our RNA-Seq data for differential exon usage and find 351 mRNAs with sex-specific isoforms.  We suggest that this new dataset will prove useful for studies focusing on C. elegans germ cell biology. Comparison of spermatogenic vs oogenic transcriptomes				
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	Ortiz	Ortiz	Noble	Sorokin	Kimble
Person First Name	Marco	Marco	Daniel	Elena	Judith
Person Mid Initials	Antonio	A		P	
Person Email	msanchez6@wisc.edu				
Person Affiliation	University of Wisconsin-Madison				
Person Address	Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin, USA				
Person Roles	submitter				
Protocol Name	P-GSE57109-4	P-GSE57109-1	P-GSE57109-3	P-GSE57109-2	
Protocol Description	Basecalls performed using CASAVA version 1.8.2 with standard parameters. We used TopHat2 v2.0.11 (with M-bM-^@M-^Sg 1 option) to align reads to the C. elegans reference genome (WBcel235.75.fa) and gene annotations (WBcel235.75.gtf), both in Wormbase WS240 (Ensembl). For compatibility to feature-counting software, we created sorted and indexed SAM versions of the BAM files (SAMtools). To create a read-count dataset, we processed SAM files with python scripts described elsewhere (Anders and Huber 2010) using gene annotations gene annotations WBcel235.75. Genome_build: WBcel235 Supplementary_files_format_and_content: Number of reads aligned per gene (wormbase)	The synchronized young adults (0-2 hours past the L4 to adult molt) were first cut behind the pharynx in PBS-Tween (0.1% Tween20) with 0.25 mM Levamisole.Gonadal arms were then cut at or near the spermatheca to isolate them from the carcass.	Total RNA was extracted from the gonads using TRIzol (Invitrogen) and RNeasy Mini Kit (Qiagen), following the manufacturer's instructions. The University of Wisconsin Biotechnology Center prepared libraries for each sample using the TruSeq Illumina sequencing protocol, which includes mRNA purification (poly-A selection) and fragmentation, cDNA synthesis, end repair, adapters ligation, and DNA fragment enrichment. Each library was bar-coded and sequenced in four different lanes to obtain single-end 101-bp reads using Illumina HiSeq2000.	The fem-3(q96gf) stocks were maintained at 15M-0C; fog-2(q71) mutants were maintained at 22M-0C. Experimental animals were syncronized and grown at 22M-0C until 2 hours after L4/Adult molt.	
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	growth protocol	
Experimental Factor Name	STRAIN	GAMETES			
Experimental Factor Type	strain	gametes			
Publication Title	A New Dataset of Spermatogenic vs. Oogenic Transcriptomes in the Nematode Caenorhabditis elegans.				
Publication Author List	Ortiz MA, Noble D, Sorokin EP, Kimble J				
PubMed ID	25060624				
Publication DOI	10.1534/g3.114.012351				
Comment[SecondaryAccession]	GSE57109				
Comment[GEOReleaseDate]	2014-07-29				
Comment[ArrayExpressSubmissionDate]	2014-04-25				
Comment[GEOLastUpdateDate]	2014-07-31				
Comment[AEExperimentType]	RNA-seq of coding RNA				
Comment[SecondaryAccession]	SRP041461				
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR1263137-SRR1263200				
SDRF File	E-GEOD-57109.sdrf.txt