characteristics.text: 2024-01-01
characteristics.characteristic: ENA first public
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: Department of Biomedical and Clinical Sciences Linköping University
characteristics.characteristic: INSDC center name
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS20894728
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-14375:S_control_3d
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: SUP-T1
characteristics.characteristic: cell_line
characteristics.text: T lymphoblast
characteristics.characteristic: cell_type
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: 5-aza-2′-deoxycytidine (Sigma-Aldrich, A3656) and GSK-3685032 (MedChemExpress, HY-139664) were dissolved in DMSO (Sigma-Aldrich, D8418) to create a stock of 10 mM. Singel-use aliquots were kept at -20°C up to 1 month. 3*105 cells per ml were treated for three or seven days with treatment being refreshed every day. RNA was extracted using Quick-DNA/RNA Kit (Zymo Research, D7001 and D7003). The manufacturer’s instructions were followed with the addition of in-column treatment with RNase A/T1 (Thermo Fisher Scientific, EN0551) and DNase I (Zymo Research, E1010). After binding of RNA to the extraction column, RNA was treated with 5U DNase for 15 minutes at room temperature. RNA was quantified using a NanoDrop 2000 spectrophotometer.  Directional total RNA sequencing libraries were prepared from 500 ng RNA using the NEBNext rRNA Depletion Kit v2 (New England Biolabs, E7405L), NEBNext Ultra™ II Directional RNA Library Prep (New England Biolabs, E7765S) and NEBNext Multiplex Oligos for Illumina (New England Biolabs, E7335S) according to the manufacturer’s instructions with slight adjustments as follows. After removal of ribosomal RNA using DNA probes and digestion with RNase H and DNase I, RNA was fragmented for 10 minutes at 94°C for an average library insert size of 300 nucleotides. First strand cDNA synthesis was performed for 10 minutes at 25°C, 50 minutes at 42°C and 15 minutes at 70°C. Libraries were PCR amplified for 9 cycles. Sequencing libraries were quantified using the Qubit 1X dsDNA High Sensitivity assay (Thermo Fisher Scientific, Q33231) and library size was estimated on a Bioanalyzer with the high sensitivity DNA assay (Agilent, 5067-4626).
characteristics.characteristic: description
characteristics.text: child
characteristics.characteristic: developmental stage
characteristics.text: childhood T acute lymphoblastic leukemia
characteristics.characteristic: disease
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: immune system
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: S_control_3d
characteristics.characteristic: title