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). Nuclei were loaded in a concentration that would result in a recovery of 10,000 nuclei. 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). Single cell ATAC-seq libraries were generated with the Chromium Single Cell ATAC V1.1 Library & Gel Bead Kit. Single cell ATAC-seq libraries were generated with the Chromium Single Cell ATAC V1.1 Library & Gel Bead Kit.
identifiers.namespace: BioSample
identifiers.id: SAMEA112721060
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: SAMEA112721060
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-12714:Lib169
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell_line
attributes.value: iPS(IMR90)-4-DL-01
attributes.tag: cell_type
attributes.value: retinal cell
attributes.tag: common name
attributes.value: human
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: disease
attributes.value: normal
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: growth condition
attributes.value: 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-12714:Lib169
attributes.tag: scientific_name
attributes.value: Homo sapiens