Comment[ArrayExpressAccession]	E-GEOD-39527
MAGE-TAB Version	1.1				
Public Release Date	2013-06-10
Investigation Title	Identification of microarray probe signals constantly present in multiple sample types (part 2)				
Comment[Submitted Name]	Identification of microarray probe signals constantly present in multiple sample types (part 2)
Experiment Description	The correlation of the RNA profiles obtained by microarray analysis was compared with that obtained from RNA-Seq by using reduced complexity sperm datasets. This resolved as a series of discordant probes. The extent of discordancy among other datasets was then determined. A correlative study between probe’s signal intensity from Illumina bead arrays with its transcript level detected by next generation sequencing technique was performed. RNAs from sperm and testis samples were applied				
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	Krawetz	Mao	Lima-Souza	Goodrich	Krawetz
Person First Name	Stephen	Shihong	Aletheia	Robert	Stephen
Person Mid Initials			C	J	A
Person Email	steve@compbio.med.wayne.edu				
Person Affiliation	Wayne State University School of Medicine				
Person Phone	313-577-6770				
Person Address	Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 275 E. Hancock, Detroit, MI, USA				
Person Roles	submitter				
Protocol Name	P-GSE39527-5	P-GSE39527-4	P-GSE39527-3	P-GSE39527-1	P-GSE39527-2
Protocol Description	Short reads were mapped to NCBI build 37.2 of the human reference genome using TopHat [7] (version 1.3.2) at paired-end base with default parameters. Alignment results were confirmed independently using Novoalign (Novocraft Technologies v.2.07). The relative abundance of each transcript as FPKM (fragments per kilobase exon per million fragments mapped) was calculated using Cufflinks [8] (version 1.1.0). Genome Build: T1.bed: hg19	Short reads were mapped to NCBI build 37.2 of the human reference genome using TopHat [7] (version 1.3.2) at paired-end base with default parameters. Alignment results were confirmed independently using Novoalign (Novocraft Technologies v.2.07). The relative abundance of each transcript as FPKM (fragments per kilobase exon per million fragments mapped) was calculated using Cufflinks [8] (version 1.1.0). Genome Build: S2_PS.bed: hg19	Short reads were mapped to NCBI build 37.2 of the human reference genome using TopHat [7] (version 1.3.2) at paired-end base with default parameters. Alignment results were confirmed independently using Novoalign (Novocraft Technologies v.2.07). The relative abundance of each transcript as FPKM (fragments per kilobase exon per million fragments mapped) was calculated using Cufflinks [8] (version 1.1.0). Genome Build: S1_PS.bed: hg19	Semen was collected then treated with PureSperm gradient centrifugation through a 50% PureSperm cushion, or Somatic Cell Lysis Buffer (0.1% sodium dodecyl sulfate [SDS], 0.5% Triton X-100).	The standard RNA-Seq libraries were prepared using the Illumina TruSeq Sample Prep Kit (Part #RS-930-2001) according to the manufacturer’s protocol. Briefly, 500 ng of total RNA was subject to two rounds of isolation and purification with oligo-dT beads (Illumina). Purified mRNA was then fragmented with divalent cations under elevated temperature. First strand cDNA synthesis was performed with random hexamers and reverse transcriptase. Second strand cDNA synthesis was performed using RNAseH and DNA PolI. Following cDNA synthesis, double stranded products were end repaired, a single base ‘A’ was added, and Illumina PE adaptors were ligated onto the cDNA products followed by 15 rounds of PCR enrichment. All samples were subject to paired-end sequencing using the Illumina Genome Analyzer (GAIIx) for 34 cycles. Image analysis, base calling, FASTQ generation and demultiplexing were performed using the genome analyzer pipeline software CASAVA (version 1.8.1).
Protocol Type	normalization data transformation protocol	normalization data transformation protocol	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol
Experimental Factor Name	SAMPLE SOURCE				
Experimental Factor Type	sample source				
Publication Title	Identification of artifactual microarray probe signals constantly present in multiple sample types.				
Publication Author List	Mao S, Souza AL, Goodrich RJ, Krawetz SA				
PubMed ID	23030061				
Publication DOI	10.2144/0000113903				
Comment[SecondaryAccession]	GSE39527				
Comment[GEOReleaseDate]	2013-06-10				
Comment[ArrayExpressSubmissionDate]	2012-07-20				
Comment[GEOLastUpdateDate]	2013-06-21				
Comment[AEExperimentType]	RNA-seq of coding RNA				
Comment[SecondaryAccession]	SRP014487				
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR525098-SRR525100				
SDRF File	E-GEOD-39527.sdrf.txt