Homo sapiens
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
ENA-FIRST-PUBLIC
2023-02-16
ENA-LAST-UPDATE
2023-02-16
External Id
SAMEA112473655
INSDC center alias
UNIVERSITY OF CALIFORNIA, BERKELEY
INSDC center name
UNIVERSITY OF CALIFORNIA, BERKELEY
INSDC first public
2023-02-16T00:15:59Z
INSDC last update
2023-02-16T00:15:59Z
INSDC status
public
Submitter Id
E-MTAB-12582:Differentiated ATRX+/+ 53
broker name
ArrayExpress
cell_line
WIBR3
cell_type
differentiated cell
common name
human
developmental stage
blastula stage
disease
normal
genotype
TP53-/-, p16-/-
phenotype
TERT overexpression
progenitor cell type
embryonic stem cell
sample name
E-MTAB-12582:Differentiated ATRX+/+ 53
scientific_name
Homo sapiens
sex
female