characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2020-11-01T04:06:22Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2019-10-16T16:36:24Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA6087401
characteristics.characteristic: External Id
characteristics.text: 1 Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway 2 Department of Infectious Diseases, Medical Clinic, St. Olavs Hospital, Trondheim, Norway
characteristics.characteristic: INSDC center name
characteristics.text: 2020-11-01T04:06:22Z
characteristics.characteristic: INSDC first public
characteristics.text: 2019-10-16T16:36:24Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS3887808
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-8444:Rep1_t42_SOX4_KO_HIV
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: SUP-T1
characteristics.characteristic: cell line
characteristics.text: T cell
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000084
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: RNA from at least 1x10^6 cells from uninfected and cells 8, 18, 30 and 42h post infection was isolated with Qiazol (Qiagen, #79306). Cells were cultured in RPMI 1640 ATCC formulation (Thermo Fisher Scientific, #A1049101) supplemented with 10% fetal bovine serum (FCS) (Thermo Fisher Scientific, #10270106), additional 0.68 nmol/ml L-glutamine (Sigma-Aldrich, #G7513-100ml), and Penicillin-Streptomycin (PenStep,\#P0781) to final 100 U/ml Penicillin and 100 µg/ml Streptomycin (Sigma-Aldrich, #P0781), and incubated at 37°C and 5% CO2. Sup-T1 cells were maintained as suspension cultures of 2x10^5 -2x10^6 cells/ml. NLENG1-IRES G1I is a full-length CXCR4-tropic molecular clone of HIV derived from pNL4-3 and carries enhanced green fluorescent protein (eGFP) inserted in front of an IRES sequence and Nef. The plasmid was a kind gift from Dr. David N. Levy, New York University College of Dentistry.1200ng p24 HIV-1 eGFP was added to 1x10^6 Sup-T1 cells in 1 ml RPMI 1640 ATCC formulation supplemented with 10% FCS, PenStrep and 10 µg/ml polybrene (Santa Cruz Biotechnology, #sc-134220). To facilitate virus attachment, spinofection was carried out by centrifugation at 1200 g for 2 hours at 20°C. The supernatant was aspirated, and the cells were cultured in complete media for the indicated time points. base calls provided by the Illumina Real-Time Analysis (RTA) software were subsequently converted into BAM format (Illumina2bam) before de-multiplexing (BamIndexDecoder) into individual, sample-specific BAM files via Illumina2bam tools (1.17.3). BAM files were converted to fastq files with BEDTools (2.27.1) and quality assessed with FastQC (0.11.7). RNA was isolated with Qiazol (Qiagen, #79306) and purified and DNAse treated on Direct-zol columns (Zymo Research, #R2052). RNA integrity was controlled using the Caliper LabChip GX (Perkin Elmer), RNA Quality Scores were found to be 10-8.16. RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using both, Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad).
characteristics.characteristic: description
characteristics.text: T cell lymphoblastic lymphoma
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0000209
characteristics.characteristic: disease
characteristics.text: Crispr-mediated SOX4 knockout
characteristics.characteristic: genotype
characteristics.text: HIV-1
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0000180
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: NLENG1-IRES G1I
characteristics.characteristic: stimulus
characteristics.text: Rep1_t42_SOX4_KO_HIV
characteristics.characteristic: title