organism: Homo sapiens
description: Protocols: 1-3 organoids of the same batch were pooled and dissociated at multiple timepoints across the organoid developmental time course. Organoids were washed three times with HBSS without Ca2+/Mg2+ (STEMCELL technologies, 37250). Single cell suspensions were obtained by adapting the protocol described in (Cowan et al. 2020) and using a papain-based dissociation kit (Miltenyi Biotec, 130-092-628). Stem cell lines were cultured in mTeSR1 (Stem Cell Technologies, 05851) with mTeSR1 supplement (Stem Cell Technologies, 05852) or mTeSR Plus (Stem Cell Technologies, 100-0274) with mTeSR Plus (Stem Cell Technologies, 100-0275) and supplemented with penicillin/streptomycin (P/S, 1:200, Gibco, 15140122) on matrigel-coated plates (Corning, 354277). Cells were split 1-2 times per week after dissociation with EDTA in DPBS (final concentration 0.5mM) (Gibco, 12605010). Media was supplemented with Rho-associated protein kinase (ROCK) inhibitor Y-27632 (final concentration 5μM, STEMCELL, 72302) the first day after thawing. To generate retinal organoids from the B7 and IMR90 lines, 600 cells were seeded in each micro-well of an agarose chamber (MicroTissues® 3D Petri Dish® micro-mold #Z764019). 409B2-iCas9 organoids were generated with 1500 cells per micro-well and treated with BMP4 (55ng/ml, Biotechne #314-BP) on day 6 with half medium change on day 9, 12 and15 (Kuwahara et al. 2015). 8,000 cells were targeted and when the cell number was not sufficient, all cells were loaded. Single cell RNA-seq libraries were generated with the Chromium Single Cell 3' V3.1 Library & Gel Bead Kit. Single cell encapsulation and library preparation were performed according to the manufacturer's protocol. Single cell RNA-seq libraries were generated with the Chromium Single Cell 3' V3.1 Library & Gel Bead Kit. Single cell encapsulation and library preparation were performed according to the manufacturer's protocol.
identifiers.namespace: BioSample
identifiers.id: SAMEA112721268
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2023-03-12
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2023-03-12
attributes.tag: External Id
attributes.value: SAMEA112721268
attributes.tag: INSDC center alias
attributes.value: D-BSSE, ETH ZURICH
attributes.tag: INSDC center name
attributes.value: D-BSSE, ETH ZURICH
attributes.tag: INSDC first public
attributes.value: 2023-03-12T00:16:40Z
attributes.tag: INSDC last update
attributes.value: 2023-03-12T00:16:40Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-12715:Lib93
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell_line
attributes.value: 409B2-iCas9
attributes.tag: cell_type
attributes.value: retinal cell
attributes.tag: common name
attributes.value: human
attributes.tag: developmental stage
attributes.value: 16 weeks
attributes.tag: disease
attributes.value: normal
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: growth condition
attributes.value: retinal organoid
attributes.tag: organism part
attributes.value: retina
attributes.tag: progenitor cell type
attributes.value: induced pluripotent stem cell
attributes.tag: progenitor organism part
attributes.value: skin
attributes.tag: sample name
attributes.value: E-MTAB-12715:Lib93
attributes.tag: scientific_name
attributes.value: Homo sapiens