title: Sample 7
organism: Mus musculus
description: Protocols: Outbred CD1 females were timed mated to generate mouse embryos of the specified stages. The morning that the vaginal plug was detected was defined as embryonic stage (e)0.5. For neural tube dissection, cervical and thoracic sections of single mouse embryos were dissected in Hanks Balanced Solution without calcium and magnesium (HBSS, Life Technologies 14185045) supplemented with 5% fetal bovine serum (FBS). The samples were then incubated on FACSmax cell dissociation solution (Amsbio T200100) with 10X Papain (30U/mg Sigma10108014001) for 11min at 37°C to dissociate the cells. To generate a single cell suspension, samples were transferred to HBSS, with 5%FBS, rock inhibitor (Y-27632 10uM, Stem Cell Technologies), and 1X non-essential amino acids (11140035), disaggregated through pipetting, and filtered once in 0.25um filters and once in 0.20um strainers (Miltenyi Biotech 130-101-812). Quality control was assayed by measuring live/cell death, cell size and number of clumps. Samples with a viability above 65% were used for sequencing. 10,000 cells per sample were used for sequencing. A suspension of 10,000 single cells was loaded onto the 10X Genomics Single Cell 3' Chip, and the dowstream cDNA synthesis was performed as per the manufacturer's protocol for the Chromium Single Cell 3' v2 Library (10X Genomics; PN-120233), to generate single cell gel beads in emulsion (GEMs). Libraries were generated following manufacturer's instructions (ChromiumTM Single Cell 3' Reagent Kits v2).
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2018-11-29T17:03:23Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2018-11-27T17:41:55Z
attributes.tag: External Id
attributes.value: SAMEA5138015
attributes.tag: INSDC center name
attributes.value: The Francis Crick Institute
attributes.tag: INSDC first public
attributes.value: 2018-11-29T17:03:23Z
attributes.tag: INSDC last update
attributes.value: 2018-11-27T17:41:55Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-7320:Sample 7
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: common name
attributes.value: house mouse
attributes.tag: developmental stage
attributes.value: embryonic day 12.5
attributes.tag: disease
attributes.value: normal
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: organism part
attributes.value: spinal cord
attributes.tag: sample name
attributes.value: E-MTAB-7320:Sample 7
attributes.tag: sampling site
attributes.value: mixed cervical and thoracic vertebrae
attributes.tag: scientific_name
attributes.value: Mus musculus
attributes.tag: strain
attributes.value: UKCrl:CD1 (ICR)