characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2022-02-01T00:15:08Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2022-02-01T00:15:08Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA12505029
characteristics.characteristic: External Id
characteristics.text: Department of Cell and Developmental Biology
characteristics.characteristic: INSDC center name
characteristics.text: 2022-02-01T00:15:08Z
characteristics.characteristic: INSDC first public
characteristics.text: 2022-02-01T00:15:08Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS10111644
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-11338:Day7_HIO_EGF_Alginate
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: To dissociate human intestinal organoids to single cells, organoids were mechanically isolated from Matrigel droplets and then tissue minced into small fragments using a scalpel in a petri dish filled with ice-cold 1X HBSS (with Mg2+, Ca2). This tissue was then transferred to a 15 mL conical tube. Dissociation enzymes and reagents from the Neural Tissue Dissociation Kit (Miltenyi, cat. no. 130-092-628) were used, and all incubation steps were carried out in a 37ºC incubator unless otherwise stated. All tubes and pipette tips used to handle cell suspensions were pre-washed with 1% BSA in HBSS to prevent adhesion of cells to the plastic. Tissue was treated for 15 minutes at 37ºC with Mix 1. Mix 2 was added to the digestion, and tissue was incubated for 10 minute increments at 37ºC until digestion was complete. After each 10 minute incubation, tissue was agitated using a P1000, and tissue digestion was visually assessed under a stereo microscope. This process continued until the tissue was fully digested. Cells were filtered through a 70 µm filter coated with 1% BSA in 1X HBSS, spun down at 500g for 5 minutes at 4ºC and resuspended in 500µl 1X HBSS (with Mg2+, Ca2+). Cells were counted using a hemocytometer, then spun down and resuspended (if necessary) to reach a concentration of 1000 cells/µL and kept on ice. Single cell droplets were immediately prepared on the 10x Chromium according to manufacturer instructions at the University of Michigan The Advanced Genomics Core, with a target of capturing 5,000-10,000 cells. Single cell libraries were prepared using the Chromium Next GEM Single Cell 3’ Library Construction Kit v3.1 according to manufacturer instructions. See Capeling et al., 2019 Stem Cell Reports \Nonadhesive Alginate Hydrogels Support Growth of Pluripotent Stem Cell-Derived Intestinal Organoids\. ENR is the standard HIO media comprised of Minigut basal media, supplemented with EGF (100 ng/ml), Noggin (100 ng/ml), and R-Spondin-2 (5% conditioned media). ENR HIOs are grown in this media for their whole life span. EGF grown HIOs are grown in ENR for the first 3 days to pattern a duodenal identity, and then are switched to minigut plus EGF (no noggin or RSPO) for the rest of their life span. Immediately after tissue dissociation, single cell libraries were prepared on the 10x Chromium with a target of 10,000 cells. Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v2, 16 rxns PN-1000075 was used. Immediately after tissue dissociation, single cell libraries were prepared on the 10x Chromium with a target of 10,000 cells. Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v2, 16 rxns PN-1000075 was used.
characteristics.characteristic: description
characteristics.text: intestinal organoid culture in alginate
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: induced pluripotent stem cell
characteristics.characteristic: progenitor cell type
characteristics.text: 7
characteristics.unit: day
characteristics.characteristic: sampling time point
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: epidermal growth factor
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0003298
characteristics.characteristic: stimulus
characteristics.text: Day7_HIO_EGF_Alginate
characteristics.characteristic: title