characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2022-12-31T00:58:24Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2022-12-31T00:58:24Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA110195613
characteristics.characteristic: External Id
characteristics.text: UGent
characteristics.characteristic: INSDC center name
characteristics.text: 2022-12-31T00:58:24Z
characteristics.characteristic: INSDC first public
characteristics.text: 2022-12-31T00:58:24Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS12293288
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-11898:G2_DOX_rep2
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: SHEP
characteristics.characteristic: cell line
characteristics.text: neuroblast (sensu Vertebrata)
characteristics.characteristic: cell type
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: 50,000 cells were harvested and spin down for 5 min at 800g. Cells were grown in RPMI1640 medium supplemented with 10% foetal bovine serum, 2 mM L-Glutamine and 100 IU/ml penicillin/streptavidin at 37°C in a 5% CO2 humid atmosphere, supplemented with 10% tetracyclin-free FBS to avoid leakage. For SOX11 inducible overexpression, the OriGene vector SC303275 containing the cDNA of SOX11 was amplified by PCR and the obtained fragment was gel purified and ligated into the opened NdeI site of response vector pLVX-TRE2G-Zsgreen1 (Takara, cat#631353) producing pLVX-TRE3G-Zsgreen1-IRES-hSOX11. The constructed plasmid was verified by restriction digest and sequenced by Sanger DNA sequencing (GATC). Lenti-X 293T Cells (Takara, cat#632180) were transfected with the regulator vector pLVX-pEF1a-Tet3G (cat#631353 and Lenti-X Packaging Single Shots (VSV-G) (cat#631275) according to the manufacturer’s instructions. The supernatant containing the lenti-virus was collected, filtered through a 0.45 µm filter and concentrated using PEG-IT. SH-EP cells were infected with the concentrated virus and 48 hours of incubation thereafter, the transduced cells were selected using 500 µg/ml G418. Individual clones were obtained by limiting dilution. After clonal expansion, the TET protein expression in each clone was checked by immunoblotting using TetR monoclonal antibody (Clone 9G9) (Clontech, cat#631131). In addition, induction of each expressing clone was tested after transduction with the pLVX-TRE3G-Luc control vector. Selected clones were transduced with lentivirus produced as described above from vector pLVX-TRE3G-Zsgreen1-IRES-hSOX11 and subsequently selected with 1 µg/ml puromycin. Each clone was treated with 1 ug/ml Doxycycline for induction of SOX11 expression or left unaffected in case of the control. ATAC-seq was performed as previously described with minor changes (Buenrostro et al. 2015). 50,000 cells were lysed and fragmented using digitonin and Tn5 transposase (Nextera DNA Library Prep Kit, cat#FC-121-1030)). Samples were purified using the DNA clean & concentrator kit from Zymo (cat#D4013). The transposased DNA fragments were amplified using the KAPA HiFi HotStart Readymix (cat#07 958 927 001) and purified using Agencourt AMPure XP beads (Beckmamn Coulter, cat#A63881). Library concentrations were measured with the Illumina Kapa Library quantification kit (Lightcycler 480 qPCR mix cat#KK4854)
characteristics.characteristic: description
characteristics.text: neuroblastoma
characteristics.characteristic: disease
characteristics.text: doxycycline-inducible SOX11 expression clone G2
characteristics.characteristic: genotype
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: bone marrow
characteristics.characteristic: organism part
characteristics.text: SOX11 overexpression
characteristics.characteristic: phenotype
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: doxycycline; 1 microgram per milliliter
characteristics.characteristic: stimulus
characteristics.text: G2_DOX_rep2
characteristics.characteristic: title