characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2022-01-01T00:13:15Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2022-01-01T00:13:15Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA10774180
characteristics.characteristic: External Id
characteristics.text: UNIVERSITY OF CALIFORNIA, IRVINE
characteristics.characteristic: INSDC center name
characteristics.text: 2022-01-01T00:13:15Z
characteristics.characteristic: INSDC first public
characteristics.text: 2022-01-01T00:13:15Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS8425441
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-11121:Retinal Organoids Day 57
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: CSC14
characteristics.characteristic: cell line
characteristics.text: induced retinal cell
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: A total of 14 RtOgs on Day 57 (D57) and 12 RtOgs on D171 were dissociated using papain-based enzymatic digestion (Worthington papain dissociation NJ, USA). Cell viability was tested with 0.4% trypan blue in a hemocytometer (>90%). The concentration was adjusted to ~870 live cells/μl for day 171 samples and ~822 cells/μl for day 57 ones. The samples were prepared for scRNA-seq library within 5 minutes. The resulting gel-in-emulsions (GEMs) were transferred to PCR tubes and incubated in a Bio-Rad C1000 Thermocycler (Bio-Rad Laboratories, Hercules, CA) for the reverse transcription protocol. The GEMs were cleaned up using Dynabeads MyOne SILANE (Life Technologies, Carlsbad CA) and then amplified using 11 cycles according the 10X workflow. The cDNA was cleaned using 0.6X SPRIselect (Beckman Coulter, Indianapolis, IN) size selection and then quality control assays using Qubit DNA HS assay (Life Technologies, Carlsbad CA) and Agilent 2100 Bioanalyzer DNA HS (Agilent, Santa Clara, CA) were performed. The endogenous cDNA fraction was then processed according to the 10X workflow for library construction. The cDNA was fragmented, end repaired and then A-tailed. After a SPRIselect cleanup the adapters were ligated on the cDNA. Sample indexes were added by PCR and a double-sided size selection using SPRIselect was performed.
characteristics.characteristic: description
characteristics.text: organoid culture
characteristics.characteristic: growth condition
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: embryonic stem cell
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0002322
characteristics.characteristic: progenitor cell type
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: Retinal Organoids Day 57
characteristics.characteristic: title