2024-12-13
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA114664856
External Id
Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences
INSDC center name
2023-11-22T22:22:51Z
INSDC last update
public
INSDC status
ERS17080799
SRA accession
E-MTAB-13562:NS_AID_KI_CTCF-AID-GFP
Submitter Id
ArrayExpress
broker name
embryonic cell line
cell_line
neural progenitor cell
cell_type
not collected
collection date
house mouse
common name
Protocols: Cells were detached with Accutase, counted and crosslinked with 1% (final) formaldehyde in their medium. Reaction was quenched with 0.125M (final) glycine, cell pellets were washed with PBS, snap frozen and stored in -80 freezer. Pellet of 10 million cells was used for CTCF ChIP experiment. ES (2i/LIF) cells were grown on gelatin-coated culture plastic in embryonic stem cells medium in the presence of MEK inhibitor (PD0325901) and GSK3 inhibition (CHIR99021) with LIF to maintain ESCs in a naive ground state. Cells were split at 80% confluence with a density of 30000 cells/sq.cm. The medium was exchanged daily. NS cells were grown on laminin-coated plates in neural differentiation medium containing N2 and B27 supplements along with recombinant murine EGF and bFGF to a final concentration of 10 ng/ml. Cells were split at 80% confluence with a density of 35000 cells/sq.cm. The medium was exchanged daily. CTCF depletion was carried out in CTCF-AID-GFP ES and NS Cells by treating with 500uM of indole acetic acid (IAA) dissolved in culture media for 24h ChIP prodecure was performed as described before (Pekowska et al., 2018, Cell). Libraries were constructed using Ovation Ultra System V2 (Tecan, 0344NB-32), according to manufacturer's instructions.
description
embryo
developmental stage
normal
disease
wild type genotype
genotype
not collected
geographic location (country and/or sea)
not applicable
isolate
Mus musculus
organism
Mus musculus
organism
inner cell mass
organism part
Mus musculus
scientific_name
NS_AID_KI_CTCF-AID-GFP
title