characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-02-19T00:22:56Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-02-19T00:22:56Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA112623582
characteristics.characteristic: External Id
characteristics.text: Ghent University
characteristics.characteristic: INSDC center name
characteristics.text: 2023-02-19T00:22:56Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-02-19T00:22:56Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS14615565
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12580:CLBGA_SOX11
characteristics.characteristic: Submitter Id
characteristics.text: 4
characteristics.unit: year
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: CLB-GA
characteristics.characteristic: cell_line
characteristics.text: neuroblast (sensu Vertebrata)
characteristics.characteristic: cell_type
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: 107 separated single cells that were cross-linked with 2% formaldehyde for 10 min at room temperature, cells were lysed. Cells were grown in RPMI1640 medium supplemented with 10% foetal bovine serum, 2mM L-Glutamine and 100 IU/ml penicillin/streptaviding at 37°C in a 5% CO2 humid atmosphere. Cross-linked DNA was digested was digested using 200U of NlaIII (NEB #R0125S) as primary restriction enzyme. This was followed by proximity ligation using 50U of T4 DNA ligase (Roche #10799009001) and ligated DNA circles were de-cross-links overnight using proteinase K and purified with NucleoMag P-Beads (Macherey-Nagel, Düren, Germany) to obtain an intermediate 3C template. To generate the 4C template, DNA was redigested using 50U DpnII (NEB #0543S) as secondary antibody followed again by proximity ligation. Digestion and ligation efficiency were evaluated via agarose gel electrophoresis. Adaptor-containing reading and non-reading primers, specific to the viewpoints of interest, were designed to amplify all captured, interacting DNA fragments (SOX11 viewpoint reading = CCACCAAAATTTTCATCATG and non-reading = TCTTCTATGCATCCGATTCT; without adapter sequence). 4C-sequencing fragments were amplified using the Expand Long Template PCR System (Roche, 11681834001) and using High Pure PCR Product Purification kit (Roche #11732676001) and QIAquick PCR Purification kit (Qiagen #28106).
characteristics.characteristic: description
characteristics.text: neuroblastoma
characteristics.characteristic: disease
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: brain
characteristics.characteristic: organism part
characteristics.text: wild type
characteristics.characteristic: phenotype
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: male
characteristics.characteristic: sex
characteristics.text: CLBGA_SOX11
characteristics.characteristic: title