Single cell RNA sequencing of 120h mouse gastruloids cultured with different doses of retinol

ABSTRACT: We quantified the effects of retinol on the cell type composition of gastruloids at 120 hours after aggregation by single cell RNA sequencing (scRNA-seq). Gastruloids were generated from the Rarb2.LacZ reporter cell line and cultured according to the standard protocol and few modifications: - culture was performed with different concentrations of retinol (0, 300, 600 nM) throughout the protocol. - culture was performed with 300 nM throughout the protocol and addition of a Mek inhibitor (1uM Mirdametinib) for the last 2 days of culture. - culture was performed with 300 nM retinol during the first 3 days and 0 nM retinol for the last 2 days. - culture was performed with 600 nM throughout the protocol and addition of a 20ng/ml FGFb for the last 2 days of culture. Additionally, gastruloids were generated with the Rarb2.LacZ cell line with a Aldh1a2−/− knockout, using the standard protocol and supplementation of 300 nM or 600 nM retinol throughout. For each retinol condition, , 40-45 gastruloids from each experimental group were collected and dissociated into single cells. Live single cells were sorted using FACS (CytoFlex SRT Beckman Coulter). DAPI-negative and singlet populations were gated and collected (Methods). Single-cell RNA sequencing of the 8 samples was done using GEM-X Universal 3’v4 chemistry with on-chip multiplexing

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Anna Alemany 

PROVIDER: E-MTAB-17398 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress