characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2022-06-15T00:13:42Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2022-06-15T00:13:42Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA10346820
characteristics.characteristic: External Id
characteristics.text: UNIVERSITY OF CAMBRIDGE
characteristics.characteristic: INSDC center name
characteristics.text: 2022-06-15T00:13:42Z
characteristics.characteristic: INSDC first public
characteristics.text: 2022-06-15T00:13:42Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS8001549
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-10639:BMP_noMEF_F2-3
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: New4f
characteristics.characteristic: cell line
characteristics.text: pluripotent stem cell
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0002248
characteristics.characteristic: cell type
characteristics.text: white-tufted-ear marmoset
characteristics.characteristic: common name
characteristics.text: Protocols: cmPSC were encapsulated in agarose microgels and transferred into conventional tissue culture plates with or without mouse embryonic fibroblasts (MEFs) in differentiation permissive, serum-free N2B27 supplemented with 1% Matrigel, 2.5% Chemically Defined Lipids (Gibco) and 1% Penicillin-Streptomycin. Signalling inhibitors and activators were then added to this base medium: FGF (bFGF, 100 ng/ml, Cambridge Stem Cell Institute), CHIR (CHIR99021, 3 µM, Cambridge Stem Cell Institute), XAV (XAV939, 3 µM, Cell Guidance Systems SM38-200), ACTA (Activin A, 20 ng/ml, Cambridge Stem Cell Institute), SB43 (SB431542, 10 µM, Tocris 1614), BMP4 (BMP4, 20 ng/ml, R&D 314-BP). For each condition, a representative pool of 20-30 microgels were randomly selected for profiling by single-cell RNA sequencing. Structures were released from microgels by incubation with 1 U/ml Agarase (Thermo Fisher Scientific, EO0461) and dissociated for 10-15 minutes in 0.25% Trypsin-EDTA (Gibco, 25200056) followed by manual dissociation in N2B27 using a blunted microcapillary pipette. Single cells were isolated manually using a microcapillary pipette, transferred immediately into 4 µl single cell lysis buffer and snap frozen. RNA separation was performed using biotinylated oligo-dT30VN-tailed oligonucleotides (IDT) conjugated to Dynabeads Streptavidin C1 in an RNAse-inhibitor supplemented buffer solution. Sequencing libraries were prepared according to an adapted version of the G&T protocol previously described. Samples were transferred to a 96-well plate and prepared for both transcriptome and methylome sequencing, by physical separation of genomic DNA (gDNA) from messenger RNA (mRNA).
characteristics.characteristic: description
characteristics.text: embryo
characteristics.characteristic: developmental stage
characteristics.text: normal
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000461
characteristics.characteristic: disease
characteristics.text: wild type genotype
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0005168
characteristics.characteristic: genotype
characteristics.text: monoculture
characteristics.characteristic: growth condition
characteristics.text: Callithrix jacchus
characteristics.characteristic: organism
characteristics.text: Callithrix jacchus
characteristics.characteristic: organism
characteristics.text: inner cell mass
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0000087
characteristics.characteristic: organism part
characteristics.text: Callithrix jacchus
characteristics.characteristic: scientific_name
characteristics.text: BMP_noMEF_F2-3
characteristics.characteristic: title