{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Anna Alemany"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15522"],"description":["We quantified the effects of retinol on the cell type composition of gastruloids with different concentrations of retinol (9, 300, 600 and 1200 nM), at 120 hours after aggregation. These gastruloids were generated from the Rarb2.LacZ reporter cell line and cultured according to the standard protocol. 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 was done with 10X chromium genomics 3' chemistry."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Sequencing of the prepared libraries on a partial lane of the illumina NovaSeq6000 S4 PE150bp. The expected sequence depth for gene expression is 20k reads/cell","Library Construction - 10X Chromium Genomics workflow was performed by polyA enrichment with single cell resolution.","Nucleic Acid Extraction - 10X Chromium Genomics workflow was performed by polyA enrichment (3').","Sample Collection - Gastruloids were collected and washed with ice-cold PBS three times. They were incubated with TrypLE Express (Gibco, 12605028) for 2X 4 min in a heating block at 37oC, shaking at 300 rpm. After incubations, the gastruloids were dissociated into single cells by pipetting up and down 10 times. The cells were washed with PBS twice, centrifuged at 1300 rpm for 5 min at 4°C, and the supernatant was carefully discarded without disturbing the pellet. The cells were resuspended in PBS containing 0,04 % BSA (Sigma-Aldrich, A3059) and 1:5000 DAPI (Invitrogen, D1306) as a viability dye. The cell suspension was filtered through a FACS  (Falcon, 352235), and FACS analysis was performed (CytoFlex SRT Beckman Coulter). DAPI-negative and singlet populations were gated and collected."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Standard 10X Genomics Cell Ranger Pipelines were run (v7.1.0) for alignment, barcode assignment and gene quantificaiton. A custom reference genome was created by adding the LazC and Neomycing genes to the standard mouse reference from 10X Genomics (refdata-gex-nn10-2020-A) according to 10X instructions."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Mus musculus"],"pubmed_authors":["Anna Alemany"],"additional_accession":[]},"is_claimable":false,"name":"Single cell RNA sequencing of 120h after aggregation mouse gastruloids cultured with different doses of retinol","description":"We quantified the effects of retinol on the cell type composition of gastruloids with different concentrations of retinol (9, 300, 600 and 1200 nM), at 120 hours after aggregation. These gastruloids were generated from the Rarb2.LacZ reporter cell line and cultured according to the standard protocol. 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 was done with 10X chromium genomics 3' chemistry.","dates":{"release":"2025-09-26T00:00:00Z","modification":"2025-09-26T01:04:51.012Z","creation":"2025-09-02T12:35:54.805Z"},"accession":"E-MTAB-15522","cross_references":{"ENA":["ERP179485"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}