characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-02-16T00:16:00Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-02-16T00:16:00Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA112473589
characteristics.characteristic: External Id
characteristics.text: UNIVERSITY OF CALIFORNIA, BERKELEY
characteristics.characteristic: INSDC center name
characteristics.text: 2023-02-16T00:16:00Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-02-16T00:16:00Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS14583642
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12582:Differentiated ATRX-/- 48
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: WIBR3
characteristics.characteristic: cell_line
characteristics.text: differentiated cell
characteristics.characteristic: cell_type
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: We used cell line WIBR3 (RRID:CVCL_9767), and human embryonic stem cells (hESCs) were collected after BrdU pulse and resuspended in nuclei staining buffer (100 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM CaCl2, 0.5 mM MgCl2, 0.1% NP-40, and 2% bovine serum albumin [Sigma-Aldrich] supplemented with 10 μg/mL Hoechst 33258 [Enzo] and 10 μg/mL propidium iodide [Sigma-Aldrich]. Single nuclei were sorted into 5 μL ProFreeze-CDM freeze medium [Lonza] + 7.5% dimethyl sulfoxide in 96-well skirted PCR plates [4titude], based on low propidium iodide (G1 phase) and low Hoechst (BrdU-induced quenching) fluorescence using an Influx cell sorter [BD Biosciences]. Strand-seq libraries were prepared using an Agilent Bravo liquid handling platform as described before (Sanders et al., 2017). For each experiment, 96 libraries were pooled and 250-450 bp-sized fragments were isolated and purified. DNA quality and concentrations were assessed using the High Sensitivity dsDNA kit [Agilent] on the Agilent 2100 Bio-Analyzer and on a Qubit 2.0 Fluorometer [Life Technologies] resp. Please refer to: doi: 10.1038/nprot.2017.029
characteristics.characteristic: description
characteristics.text: blastula stage
characteristics.characteristic: developmental stage
characteristics.text: normal
characteristics.characteristic: disease
characteristics.text: TP53-/-, p16-/-, ATRX-/-
characteristics.characteristic: genotype
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: TERT overexpression
characteristics.characteristic: phenotype
characteristics.text: embryonic stem cell
characteristics.characteristic: progenitor cell type
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: female
characteristics.characteristic: sex
characteristics.text: Differentiated ATRX-/- 48
characteristics.characteristic: title