biostudies-arrayexpressAnna AlemanyMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15527To investigate the effect of retinol on dynamic gene expression patterns during gastruloid development at different doses of retinol, we performed time-lapse bulk RNAseq during gastruloid formation. This allowed us to extract genes that have a dynamic behavior in terms of time, but also in terms of retinol metabolism.biostudies-arrayexpressNucleic Acid Extraction - After TRIzol addition, samples were dissociated using a p1000 pipette and stored at -80oC until RNA isolation. For RNA isolation, the samples were incubated at room temperature until defrosted. Standard TRIzol extraction was performed.Library Construction - RNA extraction and cDNA library preparation were performed according to the SORTseq protocol using specific CELseq2 barcodes and TruSeq small RNA adaptors. Metadata is provided in the metadata_samples.tsv file.Sequencing - By primer design, the first six bases of read 1 contained the unique molecular identifier, and the next eight bases contained the sample barcode (CELseq2), while read 2 contained the transcript information. Pair end 150 was performed.Sample Collection - Gastruloids were generated from Rarb2-LacZ mESCs reporter line with 0 nM, 300 nM, 600nM and 1200 nM retinol. E14 Rarb2-LacZ mESCs and 24 h, 48 h, 72 h, 96 h, and 120 h after aggregation; gastruloids (approximately n= 40-48 and N=3) were collected, washed with ice- cold PBS three times and 500 µl TRIzol (Thermo Fisher Scientific,15596018) was added. 2 or 3 replicates were generated for each condition.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Reads 2 with a valid barcode were selected, trimmed using TrimGalore (v.0.6.6) with default parameters, and mapped using STAR (v.2.7.7a) with default parameters to the mouse GRCm38 genome (Ensembl 102). Resulting bam files were deduplicated using umi_tools (v1.1.4) with the option “dedup --method=unique”. A count table for all samples was generated using featureCounts (v.2.0.1) from subread-2.0.1-source, with options “-t exon -g gene_name”. A data table with mtx format was also produced.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XRNA-seq of coding RNAMus musculusAnna AlemanyfalseTime-lapse RNA sequencing during gastruloid development at different concentrations of retinolTo investigate the effect of retinol on dynamic gene expression patterns during gastruloid development at different doses of retinol, we performed time-lapse bulk RNAseq during gastruloid formation. This allowed us to extract genes that have a dynamic behavior in terms of time, but also in terms of retinol metabolism.2026-07-19T00:00:00Z2026-07-19T01:00:43.275Z2025-09-02T19:54:56.472ZE-MTAB-15527ERP179524EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184