characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2022-03-31T00:18:21Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2022-03-31T00:18:21Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA13003649
characteristics.characteristic: External Id
characteristics.text: Division of Infection and Immunity University College London
characteristics.characteristic: INSDC center name
characteristics.text: 2022-03-31T00:18:21Z
characteristics.characteristic: INSDC first public
characteristics.text: 2022-03-31T00:18:21Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS10602555
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-11454:112-1
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: primary peripheral blood mononuclear cell line
characteristics.characteristic: cell line
characteristics.text: CD4-positive, alpha-beta T cell
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000624
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: To infect human primary resting CD4+ T cells with HIV-1 (pNL4.3), cells were CellTrace FarRed labeled and co-cultured with eFluo450-labelled primary CD4+ T cells either infected with HIV-1 WT, HIV-1 dVpr (pNL4.3 ΔVpr) or mock (sham) treated in the presence or absence of IL7 (20 ng/mL). After 72h of co-culture, resting target CD45RA-/CD45RO+ memory T cells were recovered by flow cytometry sorting and immediately lysed in RLT buffer. Samples were stored at -80C until extraction. Total RNA was extracted from flow cytometry sorted target memory CD4+ T cells using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions, including the on-column DNAse treatment step. For preparation of RNA-Sequencing libraries, RNA concentration was measured using the Qubit RNA High Sensitivity kit (Life Technologies) and quality checked on the 4200 Tapestation using either the High Sensitivity or standard RNA ScreenTape assay (Agilent Technologies), depending on the measured RNA concentrations. PolyA-tailed mRNA was separated for sequencing during library preparation. Libraries were prepared using KAPA’s mRNA HyperPrep kit (Roche Diagnostics) according to the manufacturer’s instructions using an input of up to 200ng and a fragmentation incubation time of 8 minutes at 94°C.
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: normal
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000461
characteristics.characteristic: disease
characteristics.text: wild type genotype
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0005168
characteristics.characteristic: genotype
characteristics.text: CD4-positive; CD45RA-negative, CD45RO-positive
characteristics.characteristic: immunophenotype
characteristics.text: Donor A
characteristics.characteristic: individual
characteristics.text: sham
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0001461
characteristics.characteristic: infect
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: organism
characteristics.text: blood component
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0001941
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: 112-1
characteristics.characteristic: title