organism: Homo sapiens
description: Protocols: Chromatin cross-linking was performed using 1% formaldehyde in PBS and quenched adding glycine to the final concentration of 125mM. Peak Calling was performed with MACS2 for ChIPseq, and Seacr 1.1 for CUT&Tag and CUTnRUN; broad peaks were called for histone marks, relaxed threshold were used for KMT2D under Seacr Immunoprecipitations were performed using 100 µg of chromatin. Antibodies used were: Ab8580 (H3K4me3), Ab8895 (H3K4me1), Ab4729 (H3K27ac), 9733B (H3K27me3). iN1 : Cortical Neurons were induced by ectopic expression of NGN2 as described by Zhang et al. 1. Cortical neuron maintenance of neurons was done with neurobasal medium fully complemented 1 and conditioned overnight on mouse astrocytes iN2 : Cortical Neurons were induced by ectopic expression of NGN2 as described by Zhang et al. 1. Cortical neuron maintenance of neurons was done with Neurobasal Plus (Thermoscientific). 1) Zhang, Y. et al. Rapid single-step induction of functional neurons from human pluripotent stem cells. TL - 78. Neuron 78 VN-r, 785–798 (2013). tracks were produced with DeepTools, as bedGraph, normalized using effective genome size (hg38) on library size (RPGC). Cells were collected with ChIP SDS buffer (0.5% SDS, 5 mM EDTA, 100mM NaCl and 50 mM Tris-HCl at pH 8.1), centrifuged 400g for 30 min and resuspended in IP buffer (0.5% SDS, 5 mM EDTA, 100mM NaCl and 50 mM Tris-HCl at pH 8.6, 1,5% Triton X-100). Chromatin was sonicated with Branson digital sonifier (Emerson Industrial Automation) to obtain bulk DNA fragments of 300 bp. Chromatin for ChIP was quantified using Bradford protein assay (Bio-Rad).
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2022-12-30
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2022-12-30
attributes.tag: External Id
attributes.value: SAMEA9348800
attributes.tag: INSDC center alias
attributes.value: Istituto Europeo di Oncologia IEO IRCSS S.r.l.
attributes.tag: INSDC center name
attributes.value: Istituto Europeo di Oncologia IEO IRCSS S.r.l.
attributes.tag: INSDC first public
attributes.value: 2022-12-30T00:23:27Z
attributes.tag: INSDC last update
attributes.value: 2022-12-30T00:23:27Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-10561:S26150_KAB_7G_KMT2D
attributes.tag: age
attributes.value: 5
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell_line
attributes.value: iN2
attributes.tag: cell_type
attributes.value: cortical neuron
attributes.tag: common name
attributes.value: human
attributes.tag: developmental stage
attributes.value: juvenile stage
attributes.tag: disease
attributes.value: Kabuki syndrome
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: individual
attributes.value: KAB7
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: organism part
attributes.value: skin
attributes.tag: progenitor cell typecell type
attributes.value: induced pluripotent stem cell
attributes.tag: sample name
attributes.value: E-MTAB-10561:S26150_KAB_7G_KMT2D