characteristics.text: 2024-12-27
characteristics.characteristic: ENA first public
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: SAMEA115057206
characteristics.characteristic: External Id
characteristics.text: Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen
characteristics.characteristic: INSDC center name
characteristics.text: 2023-12-22T11:29:27Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS17597702
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-13660:APST
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: stem cell derived cell line (post-implantation epiblast stem cell)
characteristics.characteristic: cell_line
characteristics.text: anterior end of the primitive streak
characteristics.characteristic: cell_type
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: Cells were collected in TC lab, and Eomes-GFP were sorted by FACS Single cells from either in vitro-differentiated cells or transgenic embryos were sorted into Eppendorf Polypropylene U-shaped 384-well Twin Tec PCR Microplates (Thermo Fisher Scientific, 10573035), containing 2 μl of lysis solution (0.2% (v/v) Triton X-100) supplemented with 0.4 U/μl RNasin Ribonuclease Inhibitor (Promega, N2515) and 400 nM indexed RT primer from group 1 (1-96 barcodes) or group 2 (97-192 barcodes) as described in Mariani et al., 2021. Capture plates were prepared on the Bravo automated liquid handling robot station (Agilent) using 384-filtered tips (Axygen, 302-82-101). Index sorting was performed using either a FACS Aria III cell sorter (BD Biosciences) or a SONY SH800S cell sorter (Sony Biotechnology) at the DanStem/reNEW Flow Cytometry Platform (University of Copenhagen, Denmark), gating in SSC-A versus FSC-A to collect live cells, and then in FSC-W versus FSC-A to sort only singlets. For in vivo experiments, only GFPpos cells were sorted to capture Eomes-expressing cell types. Immediately after sorting, plates were spun down, snap-frozen on dry ice, and stored at -80°C until further processing. Semi-automated library preparation was performed as described in Jaitin et al., 2014, using 10-12 cycles of PCR amplification and AMPure XP beads (Beckman Coulter™Agencourt: A63881) for purification. DNA concentration was measured with a Qubit Fluorometer (Thermo Fisher Scientific, Q32854), and fragment size was determined with a Fragment analyzer (Advanced Analytical).
characteristics.characteristic: description
characteristics.text: epiblast to anterior primitive streak
characteristics.characteristic: developmental stage
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: anterior primitive streak
characteristics.characteristic: organism part
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: 129
characteristics.characteristic: strain
characteristics.text: APST
characteristics.characteristic: title