biostudies-arrayexpressGiulia PiccoMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15618Haematopoietic and endothelial cells derive from a subset of Flk-1 expressing cells. In vitro differentiation of mouse embryonic stem cells (mESCs) to embryoid bodies (EBs) recapitulate several aspects of early embryonic development. We previously identified three candidate uncharacterized Riken genes (I830077J02Rik, C130074G19Rik and A530016L24Rik) potentially important for the cell lineage commitment toward haematopoietic precursors. Here, we investigate the transcriptomic profiles of cells depleted for these genes at day 7 of embryoid body differentiation, by scRNA-seq.biostudies-arrayexpressNucleic Acid Extraction - Viable single cells (18000 per run, with an estimated recovery of 10000 cells) were encapsulated for cDNA synthesis and barcoded on a Chromium X using the Chromium Single Cell G Chip and final libraries were generated using the 10X Chromium Next GEM Single Cell 3’ kit v3.1 (10X Genomics) and instructions.Library Construction - Final libraries were generated using the 10X Chromium Next GEM Single Cell 3’ kit v3.1 (10X Genomics) and instructions. Quality and quantity of the sequence libraries were determined with a High Sensitivity DNA kit using an Agilent 2100 Bioanalyzer (Agilent).Sample Collection - Embryoid bodies at day 7 (D7) of differentiation were washed three times with PBS by spinning at 1000 rpm for 5 minutes, and dissociated using TrypLE (Gibco, 12604013) in a 37°C water bath while shaking with intermitting pipetting to facilitate dissociation. After 5 minutes, Trypsin/EDTA was added and dissociation continued for another 1 minute while pipetting. The dissociation was inactivated with PBS supplemented with 10% FBS (PBS-FBS), strained with a 40 µM cell strainer, washed three times with PBS-FBS by centrifuging at 300 rpm for 10 minutes and prepared for downstream applications.Sequencing - Libraries were sequenced on a Novaseq 6000 system (Illumina), using an S2 v1.5 100 cycles flow cell (Illumina) with run settings of 28-10-10-90 cycles, followed by computational alignment using CellRanger 7.1.0 software (10X Genomics)OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Sequencing reads were processed using the CellRanger 7.1.0 software (10X Genomics) and aligned to the mouse mm10 reference genome (mm10-1.2.0).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNA from single cellsMus musculusGiulia PiccofalseSingle-cell RNA-sequencing of wild-type, I830077J02Rik, C130074G19Rik and A530016L24Rik gene knockouts at day 7 of embryoid body differentiationHaematopoietic and endothelial cells derive from a subset of Flk-1 expressing cells. In vitro differentiation of mouse embryonic stem cells (mESCs) to embryoid bodies (EBs) recapitulate several aspects of early embryonic development. We previously identified three candidate uncharacterized Riken genes (I830077J02Rik, C130074G19Rik and A530016L24Rik) potentially important for the cell lineage commitment toward haematopoietic precursors. Here, we investigate the transcriptomic profiles of cells depleted for these genes at day 7 of embryoid body differentiation, by scRNA-seq.2026-01-14T00:00:00Z2026-04-15T22:08:50.529Z2025-09-22T15:56:55.764ZE-MTAB-15618ERP180452EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0003816EFO_0004184