MAGE-TAB Version 1.1 Investigation Title RNA-seq of liver stage-derived parasites from wild-type and TCRδ-/- mice Experimental Design genetic modification design Experimental Design Term Source REF EFO Experimental Design Term Accession Number EFO_0001758 Experimental Factor Name growth condition Experimental Factor Type growth condition Experimental Factor Term Source REF EFO Experimental Factor Term Accession Number EFO_0000523 Person Last Name Neves Pamplona Person First Name Daniel Ana Person Mid Initials Person Email dneves@igc.gulbenkian.pt anapamplona@medicina.ulisboa.pt Person Phone Person Fax Person Affiliation Instituto Gulbenkian de Ciência, Oeiras, Portugal Instituto de Medicina Molecular João Lobo Antunes, Lisboa, Portugal Person Address Rua da Quinta Grande, 6 2780-156 Oeiras Portugal Faculdade de Medicina da Universidade de Lisboa Av. Professor Egas Moniz 1649-028 Lisboa Portugal Person Roles submitter investigator Person Roles Term Source REF Person Roles Term Accession Number Quality Control Type Quality Control Term Source REF Quality Control Term Accession Number Replicate Type Replicate Term Source REF Replicate Term Accession Number Normalization Type Normalization Term Source REF Normalization Term Accession Number Date of Experiment 2015-10-01 Public Release Date 2019-04-11 PubMed ID Publication DOI Publication Author List Publication Title Publication Status Publication Status Term Source REF Publication Status Term Accession Number Experiment Description P. berghei ANKA parasites were collected from the blood at 74h after infection of wild-type and TCRδ-/- mice with 2x10^4 sporozoites (samples were pooled from 3 mice/ group) and mRNA was sequenced by RNA-seq. Protocol Name P-MTAB-83815 P-MTAB-83816 P-MTAB-83813 P-MTAB-83814 Protocol Type nucleic acid library construction protocol nucleic acid sequencing protocol sample collection protocol nucleic acid extraction protocol Protocol Term Source REF EFO EFO EFO EFO Protocol Term Accession Number EFO_0004184 EFO_0004170 EFO_0005518 EFO_0002944 Protocol Description Barcoded stranded mRNA-seq libraries were prepared using the Illumina TruSeq kit implemented on the liquid handling robot Beckman FXP2. Libraries were pooled in equimolar amounts and loaded on the sequencer HiSeq 2000 and sequenced bi-directionally, 100 bases from each end. The 6 samples were sequenced on one lane of HiSeq2000. Male Tcr delta-deficient mice (Tcrdtm1Mom) (TCRdelta-/-) and wild-type C57BL/6 mice, of ages 6-8 weeks old, were infected with intravenous (i.v.) inoculation of 2x10^4 GFP-expressing P. berghei ANKA sporozoites purified from mosquito salivary glands. Parasites were collected from the blood at exactly 74 hours after sporozoites infection, at the late trophozoite stage of development. Samples were pooled from 3 mice/ group. DNA was removed with a TURBO DNA-free Kit (Applied Biosystems).​ Protocol Parameters Protocol Hardware Illumina HiSeq 2000 Protocol Software Protocol Contact Term Source Name EFO ArrayExpress Term Source File http://www.ebi.ac.uk/efo/ http://www.ebi.ac.uk/arrayexpress/ Term Source Version 2.38 SDRF File E-MTAB-6493.sdrf.txt Comment [TemplateType] High-throughput sequencing Comment [Submitted Name] RNA-seq of liver stage-derived parasites from wild-type and TCRδ-/- mice Comment [SecondaryAccession] ERP114213 Comment [SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/ERR3210516-ERR3210521 Comment [AEExperimentType] RNA-seq of coding RNA Comment[ArrayExpressAccession] E-MTAB-6493