MAGE-TAB Version 1.1 Investigation Title [10x] scRNA-seq of mouse Plasmodium-specific CD4+ T cells Experimental Design disease state design time series design Experimental Design Term Source REF EFO EFO Experimental Design Term Accession Number EFO:0001756 EFO:0001779 Experimental Factor Name infect time compound dose Experimental Factor Type infect time compound dose Experimental Factor Term Source REF EFO Experimental Factor Term Accession Number EFO_0000721 Person Last Name Lee Person First Name Hyun Jae Person Mid Initials Person Email hyun.lee89@gmail.com Person Phone Person Fax Person Affiliation The Peter Doherty Institute for Infection and Immunity, University of Melbourne Person Address 792 Elizabeth St, Melbourne VIC 3000, Australia Person Roles submitter 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 2019-04-19 Public Release Date 2020-10-14 PubMed ID Publication DOI Publication Author List Publication Title Publication Status Publication Status Term Source REF Publication Status Term Accession Number Experiment Description Plasmodium-specific CD4+ T cells from mice infected with Plasmodium chabaudi chabaudi AS parasites were recovered at Days 0, 7, and 28 to undergo processing and generate scRNA-seq dataset. At Day 28, mice were administered with either saline or artesunate (intermittent artesunate therapy - IAT). scRNA-seq dataset was analysed to investigate transcriptome dynamics of CD4+ T cells from effector to memory states. Protocol Name P-MTAB-99272 P-MTAB-99271 P-MTAB-99270 P-MTAB-99269 P-MTAB-99268 Protocol Type high throughput sequence alignment protocol nucleic acid sequencing protocol nucleic acid library construction protocol nucleic acid extraction protocol sample collection protocol Protocol Term Source REF EFO EFO EFO EFO EFO Protocol Term Accession Number EFO_0004917 EFO_0004170 EFO_0004184 EFO_0002944 EFO_0005518 Protocol Description For the BGI FASTQ files to be made compatible with “cellranger count” pipeline from Cell Ranger version 3.0.2 (10x Genomics), file names and FASTQ headers were reformatted using code from https://github.com/IMB-Computational-Genomics-Lab/BGIvsIllumina_scRNASeq 69. Data was processed using 10x mouse genome 1.2.0 release as a reference. Sequencing of single cell libraries was performed using a MGISEQ-2000 instrument (BGI). Sequencing libraries were prepared using Single Cell 3’ Reagent Kits v3 (10x Genomics) and then converted using the the MGIEasy Universal Library Conversion Kit (BGI). PbTII cells were then sorted as single-cells using the Chromium 10X Genomics platform. Approximately 8,000 cells were loaded per channel onto a Chromium controller (10x Genomics) for generation of gel bead-in-emulsions using 10x Genomics Single Cell 3' Reagent Kit v3. PbTII cells from the spleen were isolated by flow cytometry into a 1% BSA/PBS buffer. For D7 and D28 timepoints, five recipient mice were pooled for isolating splenic PbTII cells. Protocol Parameters Protocol Hardware BGISEQ-500 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-9317.sdrf.txt Comment [Submitted Name] [10x] scRNA-seq of mouse Plasmodium-specific CD4+ T cells Comment [TemplateType] Animal - Single-cell sequencing Comment [SecondaryAccession] ERP122951 Comment [SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/ERR4350153-ERR4350156 Comment [AEExperimentType] RNA-seq of coding RNA from single cells Comment[ArrayExpressAccession] E-MTAB-9317