characteristics: ERC000011
characteristics: ENA-CHECKLIST
characteristics: 2022-10-03T13:36:26Z
characteristics: ENA-FIRST-PUBLIC
characteristics: 2022-10-03T13:36:26Z
characteristics: ENA-LAST-UPDATE
characteristics: SAMEA110468059
characteristics: External Id
characteristics: ETH Zurich, DBSSE
characteristics: INSDC center name
characteristics: 2022-10-03T13:36:26Z
characteristics: INSDC first public
characteristics: 2022-10-03T13:36:26Z
characteristics: INSDC last update
characteristics: public
characteristics: INSDC status
characteristics: ERS12566087
characteristics: SRA accession
characteristics: E-MTAB-12004:Day15_B7_WTC_409B2_WIBJ2_HOIK1_RNA
characteristics: Submitter Id
characteristics: ArrayExpress
characteristics: broker name
characteristics: 201B7, GM25256, 409B2, HPSI0314i-hoik_1, HPSI0214i-wibj_2
characteristics: cell_line
characteristics: human
characteristics: common name
characteristics: Protocols: Single cell suspensions were acquired by dissociation of the organoids with a papain-based dissociation (Miltenyi Biotec, 130-092-628). For 19 days of development, cerebral organoids were generated from five different stem cell lines: three human induced pluripotent stem cell lines 201B7 (B7), GM25256 (WTC), HPSI0214i-kucg_2 (Kucg2), and two human embryonic stem cell line H1-hESC (H1), HES-3 simultaneously. The genotype was PAX6YFP for H1 cells, and NKX2.1GFP for HES-3 cells. For 15 days of development, cerebral organoids were generated from five human induced pluripotent stem cell lines 201B7 (B7), GM25256 (WTC), 409B2, HPSI0314i-hoik_1 (Hoik1), HPSI0214i-wibj_2 (Wibj2). Cerebral organoids were generated using a whole brain organoid differentiation protocol (Lancaster et al. 2013). For scATAC-seq, nuclei were isolated according to the protocol provided by 10x genomics (Demonstrated protocol CG000169 Rev D) using the low input protocol and a lysis time of 3 min. Nuclei were loaded in a concentration that would result in a recovery of 10,000 nuclei. In case of less nuclei recovered, the maximum number of nuclei was targeted. For sc-RNAseq, cells were put in a concentration after counting and viability checking that allowed targeting 10,000 cells and in case the cell number was not sufficient all cells were loaded. After dissociation, cell viability was checked, cells were counted and 7000 cells were targeted per lane of the 10x microfluidic chip. Single cell ATACseq libraries were generated with the Chromium Single Cell ATAC V1 Library & Gel Bead Kit. Single cell RNAseq libraries were generated with the Chromium Single Cell 3’ V3 Library & Gel Bead Kit and sequenced on Illumina’s HiSeq platform.
characteristics: description
characteristics: normal
characteristics: disease
characteristics: wild type genotype
characteristics: genotype
characteristics: cerebral organoid culture
characteristics: growth condition
characteristics: Homo sapiens
characteristics: organism
characteristics: Homo sapiens
characteristics: organism
characteristics: skin
characteristics: organism part
characteristics: induced pluripotent stem cell
characteristics: progenitor cell type
characteristics: Homo sapiens
characteristics: scientific_name
characteristics: Day15_B7_WTC_409B2_WIBJ2_HOIK1_RNA
characteristics: title