MAGE-TAB Version 1.1 Investigation Title Bulk ATAC-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 time infect treatment Experimental Factor Type time infect treatment 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 2018-09-18 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 to generate ATAC-seq dataset (2 independent biological repeats per time point). At Day 28, mice were administered with either saline or artesunate (intermittent artesunate therapy - IAT). Bulk ATAC-seq dataset was analysed to investigate epigenomic landscapes of CD4+ T cells from effector to memory states. Protocol Name P-MTAB-99436 P-MTAB-99437 P-MTAB-99438 P-MTAB-99439 P-MTAB-99435 P-MTAB-99440 Protocol Type nucleic acid extraction protocol nucleic acid library construction protocol nucleic acid sequencing protocol normalization data transformation protocol sample collection protocol high throughput sequence alignment protocol Protocol Term Source REF EFO EFO EFO EFO EFO EFO Protocol Term Accession Number EFO_0002944 EFO_0004184 EFO_0004170 EFO_0003816 EFO_0005518 EFO_0004917 Protocol Description Supernatant was removed and 50 µl of transposase mixture (25 µl TD buffer (Illumina), 2.5 µl of TDE1 (Illumina), 0.5 µl of 1% digitonin (Promega), 22 µl nuclease-free water) added to the cells. Cells were then incubated at 37°C for 30 min at 300 rpm in an Eppendorf ThermoMixer. Transposed DNA was amplified and purified using a QIAGEN MinElute PCR Purification kit, according to the manufacturer’s protocol. Purified DNA was eluted in 20 µl Buffer EB (QIAGEN) and sequenced using paired-end sequencing on a NextSeq 550 instrument (Illumina). Unmapped reads, reads mapping to unassigned contigs and mate unmapped reads were removed, as well as mitochondrial genes and PCR duplicates. The resulting .bam files were first converted to bedGraph using the bedtools genomecov command from the BEDTools suite and then converted to bigwig format using the bedGraphToBigWig program from University of California, Santa Cruz (UCSC) Genome Browser (https://genome.ucsc.edu/). Read counts were normalised to the number of uniquely mapped reads per million. Fast-ATAC sequencing was performed as previously described (Corces et al. 2016). Briefly, 5,000 viable PbTII cells were sorted by flow cytometry and pelleted by centrifugation. Raw ATAC-seq reads were mapped to mouse genome MGSCv37 (mm9) using BWA-MEM. Protocol Parameters Protocol Hardware NextSeq 550 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-9393.sdrf.txt Comment [TemplateType] Animal - High-throughput sequencing Comment [Submitted Name] Bulk ATAC-seq of mouse Plasmodium-specific CD4+ T cells Comment [SecondaryAccession] ERP123050 Comment [SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/ERR4368613-ERR4368620 Comment [AEExperimentType] ATAC-seq Comment[ArrayExpressAccession] E-MTAB-9393