characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-10-24T21:00:29Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-10-24T21:00:29Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA110177254
characteristics.characteristic: External Id
characteristics.text: Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute; Science for Life Laboratory, Sweden
characteristics.characteristic: INSDC center name
characteristics.text: 2023-10-24T21:00:29Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-10-24T21:00:29Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS12276062
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-11858:ctrl_rep1
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: HAP1
characteristics.characteristic: cell_line
characteristics.text: fibroblast
characteristics.characteristic: cell_type
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: Cells were harvested at 80% to 90% confluency. 1,000,000-5,000,000 cells were pelleted and lysed in 700 μL Qiazol (QIAGEN). 140 μL chloroform were added. The mixture was shaken for 30 sec and incubated for 2.5 min at room temperature, followed by centrifugation at 9,000×g for 5 min at 4°C. The upper aqueous phase was mixed with 1 volume isopropanol thoroughly, followed by 10 min incubation at room temperature. The RNA was pelleted by centrifugation at 9,000×g for 10 min at 4°C and washed once with ice-cold 70 % ethanol. RNA concentration and purity were determined by nanodrop (Nanodrop 2000c). To remove genomic DNA, 10 μg RNA were mixed with 5 μL 10×TurboDNase buffer (Invitrogen), 1 μL TurboDNase (Invitrogen), 1 μL RNase Inhibitor (RiboLock, Invitrogen), and water was added to a total volume of 50 μL. The samples were incubated at 37°C for 30 min and purified with the Zymo RNA Clean & Concentrator Kit (Zymo Research). The concentration of purified RNA was determined by Qubit, and the integrity was assessed on an Agilent Bioanalyzer instrument with RNA 6000 Nano kit according to the manufacturer’s protocol. The RNA was first enriched for molecules with PolyA tail with NEBNext® Poly(A) mRNA Magnetic Isolation Module. The RNA library preparation was performed using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s instruction.
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: chronic myeloid leukemia
characteristics.characteristic: disease
characteristics.text: wild type (transfected with empty Cas9 vector)
characteristics.characteristic: genotype
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: bone marrow
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: ctrl_rep1
characteristics.characteristic: title