title: NS_AID_KI_CTCF-AID-GFP_IAA
organism: Mus musculus
description: 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.
attributes.tag: ENA first public
attributes.value: 2024-12-13
attributes.tag: External Id
attributes.value: SAMEA114664857
attributes.tag: INSDC center name
attributes.value: Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences
attributes.tag: INSDC last update
attributes.value: 2023-11-22T22:22:51Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-13562:NS_AID_KI_CTCF-AID-GFP_IAA
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell_line
attributes.value: embryonic cell line
attributes.tag: cell_type
attributes.value: neural progenitor cell
attributes.tag: collection date
attributes.value: not collected
attributes.tag: common name
attributes.value: house mouse
attributes.tag: developmental stage
attributes.value: embryo
attributes.tag: disease
attributes.value: normal
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: geographic location (country and/or sea)
attributes.value: not collected
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: organism part
attributes.value: inner cell mass
attributes.tag: sample name
attributes.value: E-MTAB-13562:NS_AID_KI_CTCF-AID-GFP_IAA
attributes.tag: scientific_name
attributes.value: Mus musculus