Comment[ArrayExpressAccession]	E-GEOD-55035
MAGE-TAB Version	1.1		
Public Release Date	2014-04-28
Investigation Title	Gene expression differences underlying genotype-by-genotype specificity in a host-parasite system		
Comment[Submitted Name]	Gene expression differences underlying genotype-by-genotype specificity in a host-parasite system
Experiment Description	Expression of bumblebees (Bombus terrestris) from four colonies exposed to 3 different genotypes of the trypanosome parasite Crithidia bombi RNA from guts of exposed individuals. Sacrificed 18hr after exposure.		
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	Barribeau	Barribeau	Schmid-Hempel
Person First Name	Seth	Seth	Paul
Person Email	seth@env.ethz.ch		
Person Affiliation	ETH Zürich		
Person Address	Institute of Integrative Biology, ETH Zürich, Universitatstrasse 16, Zürich, Canton of Zurich, Switzerland		
Person Roles	submitter		
Protocol Name	P-GSE55035-2	P-GSE55035-1	
Protocol Description	remove reads with adaptors, remove reads with unknown nucleotides larger than 5%, remove reads with low quality (more than half of the bases' qualities are less than 5) Obtain clean reads SOAP2 mapping to genome Analysis- Genome Mapping -SOAPsplice, SOAP Software- TopHat, Release 1.9, Release 2.21, -s 40 -l 32 -v 3 -r 2 Genome_build: Bter_1.1	qiagen Rneasy RNA extraction Beads with oligo(dT) were used to isolate poly(A) mRNA after total RNA was collected from eukaryote (prokaryocyte can be treated with kit to remove rRNA before next step). Fragmentation buffer was added for interrupting mRNA to short fragments. Taking these short fragments as templates, Random hexamer-primer were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I, respectively. Short fragments were purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding poly(A). After that, the short fragments were connected with sequencing adaptors. And, for amplification with PCR, we selected suitable fragments, as templates, with respect to the result of agarose gel electrophoresis. At last, the library could be sequencing using Illumina HiSeq™ 2000.	
Protocol Type	normalization data transformation protocol	nucleic acid library construction protocol	
Experimental Factor Name	COLONY	TREATMENT	
Experimental Factor Type	colony	treatment	
Publication Title	Gene expression differences underlying genotype-by-genotype specificity in a host-parasite system.		
Publication Author List	Barribeau SM, Sadd BM, du Plessis L, Schmid-Hempel P		
PubMed ID	24550506		
Publication DOI	10.1073/pnas.1318628111		
Comment[SecondaryAccession]	GSE55035		
Comment[GEOReleaseDate]	2014-04-28		
Comment[ArrayExpressSubmissionDate]	2014-02-14		
Comment[GEOLastUpdateDate]	2014-04-28		
Comment[AEExperimentType]	RNA-seq of coding RNA		
Comment[AdditionalFile:Data1]	GSE55035_Bombus_terrestris.Gene.rpkm.txt		
Comment[SecondaryAccession]	SRP037972		
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR1169734-SRR1169749		
SDRF File	E-GEOD-55035.sdrf.txt