characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2020-02-29T04:05:15Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2019-10-21T16:33:18Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA6104722
characteristics.characteristic: External Id
characteristics.text: Department of Oncology and Hemato-Oncology, University of Milan, Italy
characteristics.characteristic: INSDC center name
characteristics.text: 2020-02-29T04:05:15Z
characteristics.characteristic: INSDC first public
characteristics.text: 2019-10-21T16:33:18Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS3905402
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-8455:7DupASD1.sh1
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: neural stem cell
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000047
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: Differentiation into NCSCs was performed as previously described (67), with the exception of NCSCs used in the experiment reported in Fig. 1D-F (16). WBS1, WBS2, WBS3, WBS4, 7dupASD1, AtWBS1 and CTL2 fibroblasts were reprogrammed using the mRNA Reprogramming kit (Stemgent), while the 7dupASD2 and CTL1R lines were reprogrammed with the microRNA Booster kit (Stemgent). The CTL3 line was reprogrammed by transfection with the STEMCCA polycistronic lentiviral vector followed by Cre-mediated excision of the integrated polycistron. 7dupASD3 and CTL4R fibroblasts were reprogrammed using the SimpliconTM RNA Reprogramming kit (Millipore). Prior to differentiation, iPSC lines were cultured on hESC-qualified Matrigel (BD Biosciences) coated plates, diluted 1:40 in DMEM/F-12 and grown in mTeSR-1 medium (StemCell Technologies). They were passaged upon treatment with Accutase (Sigma) and then plated in mTeSR-1 medium supplemented with 5μM Y-27632 (Sigma). Differentiation into NCSCs was performed as previously described (67), with the exception of NCSCs used in the experiment reported in Fig. 1D-F (16). RNA was extracted using the RNeasy Micro Plus kit (Qiagen) according to manufacturer’s instructions. Retrotranscribed cDNA was obtained from 0.5-1 μg of total RNA using the SuperScript VILO Retrotranscription kit (Thermo Fisher Scientific). RT-qPCR was performed on a 7500 Fast Real-Time PCR system (Applied Biosystems) using SYBR Green Master Mix (Applied Biosystems) as detecting reagent. A total cDNA amount corresponding to 15 ng of starting RNA was used for each reaction. Each sample was analyzed in triplicate and normalized to GAPDH. Relative mRNA quantity was calculated by the comparative cycle threshold (Ct) method using the formula 2-deltaCt. BAZ1B: CCTCGCAGTAAGAAAGCAAAC (forward); ACTCATCCAGCTCCTTTTGAC (reverse). 4 GAPDH: GCACCGTCAAGGCTGAGAAC (forward); AGGGATCTCGCTCCTGGAA (reverse). NR2F1: AGAAGCTCAAGGCGCTACAC (forward); GGGTACTGGCTCCTCACGTA (reverse). NR2F2: GCAAGTGGAGAAGCTCAAGG (forward); GCTTTCCACATGGGCTACAT (reverse). TFAP2A: GCCTCTCGCTCCTCAGCTCC (forward); CGTTGGCAGCTTTACGTCTCCC (reverse). SOX9: AGTACCCGCACTTGCACAAC (forward); GTAATCCGGGTGGTCCTTCT (reverse). Library preparation for RNA sequencing was performed according to TruSeq Total RNA sample preparation protocol (Illumina), starting from 250 ng - 1 μg of total RNA. cDNA library quality was assessed at an Agilent 2100 Bioanalyzer, using the High sensitivity DNA kit.
characteristics.characteristic: description
characteristics.text: adult
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0001272
characteristics.characteristic: developmental stage
characteristics.text: 7q11.23 microduplication syndrome
characteristics.characteristic: disease
characteristics.text: wild type genotype
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0005168
characteristics.characteristic: genotype
characteristics.text: 7DupASD1
characteristics.characteristic: individual
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: organism
characteristics.text: skin
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0000014
characteristics.characteristic: organism part
characteristics.text: induced pluripotent stem cell
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0004905
characteristics.characteristic: progenitor cell type
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: 7DupASD1.sh1
characteristics.characteristic: title