characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-10-13T20:40:13Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-10-13T20:40:13Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA113611962
characteristics.characteristic: External Id
characteristics.text: Division of Newborn Medicine and Epigenetics Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
characteristics.characteristic: INSDC center name
characteristics.text: 2023-10-13T20:40:13Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-10-13T20:40:13Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS15606138
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-7551:set1-Mutant_day14
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: fibroblast
characteristics.characteristic: cell_type
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: Total RNA was isolated using the TRIZOL reagent according to the manufacturer’s instructions (Life Technologies cat no: 15596018). Human iPSC were cultures on irradiated mouse embryonic fibroblast (MEF) feeder cells CF-1 (GlobalStem cat no:GSC-6201G) in DMEM/F12-15mM Hepes (STEMCELL Technologies cat no: 36254) supplemented with 20% KnockOut Serum Replacement (KSR) (Invitrogen cat no:10828-028), 100 mM 2-mercaptoethanol (2ME) (Gibco Cat no: 21985-023), 2mM L-glutamine (corning cat no:25-005-CI), 1XMEM non-essential amino acids (Invitrogen Cat.no:11140050) and 10 ng/ml bFGF (Bio Pioneer Inc cat no: HRP-0011-1). Cells were fed, inspected daily and differentiated cells at the edges of colonies were mechanically removed. Cells were passaged either manually or with collagenase (Invitrogen cat no: 17104-019). The neuronal differentiation was performed according to: Yichen Shi et al., under the title \"Directed differentiation of human pluripotent stem cells to cerebral cortex neurons and neural networks\" published in Nature protocols, 2012 To generate footprint-free genotypically-matched controls, we corrected the KDM5C mutation to the WT sequence using CRISPR/Cas9 and PiggyBac technologies (Yusa, K. Seamless genome editing in human pluripotent stem cells using custom endonuclease-based gene targeting and the piggyBac transposon. Nat Protoc 8, 2061–2078 (2013). The neuronal differentiation was performed according to: Yichen Shi et al., under the title \"Directed differentiation of human pluripotent stem cells to cerebral cortex neurons and neural networks\" published in Nature protocols, 2012 Nucleic acids were exctracted according to NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® according to manufacture guidelines. (New England BioLabs cat no: E7420L) Library preparation was performed using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® according to manufacture guidelines. (New England BioLabs cat no: E7420L and E7490L, E7335L).
characteristics.characteristic: description
characteristics.text: intellectual disability
characteristics.characteristic: disease
characteristics.text: KDM5C c.2T>C
characteristics.characteristic: genotype
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: donor 1
characteristics.characteristic: individual
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: skin
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: male
characteristics.characteristic: sex
characteristics.text: set1-Mutant_day14
characteristics.characteristic: title