{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Ridvan Cetin"],"organism":["Mus musculus"],"software":["CellRanger"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16347"],"description":["An in vitro differentiation system using mouse embryonic stem cells to capture multiple differentiation timepoints: days 3, 4, 5, 6, and 7 as scMultiome (ATAC+RNA) and days 0, 2, and 4 as scRNA-seq. scMultiome libraries were generated using the Single Cell Multiome ATAC + Gene Expression v1 chemistry, and scRNA-seq libraries were generated using the Single Cell 3' v3 chemistry. Nuclei isolation for scMultiome was performed using a modified 0.1X lysis protocol from 10x Genomics protocol CG000366, with the digitonin concentration adjusted from 0.001% to 0.005%."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Day 0,2,3,4,5,6,7, and 8 differentiated mouse embryonic stem cells are collected as embryonic bodies, washed with PBS, dissociated with TrypLE Express Enzyme for 5 minutes, and Trypsin-EDTA for 3 minutes at 37°C in intermittent pipetting. After dissociation, samples are inactivated with PBS+10%FCs, go through a filter (40 μm), and spin down at 1000rpm for 5 minutes. The samples were washed three times with PBS containing 10% FCS. Then, DNase Treatment protocol followed by the manufacturer's recommendations. 10X Genomics 'Single Cell Multiome ATAC + Gene Expression v1' and Single Cell 3' v3 chemistery and protocol used as recomended.","Growth Protocol - mESCs-Medium: DMEM HyClone™ (cytiva SH30081), 15% - Fetal Bovine Serum (FBS) (Capricorn Scientific FBS-12A, CP18-2152), 1X - MEM Non-Essential Amino Acids Solution (100X) (Gibco 11140-035), 2mM - GlutaMAX™ Supplement (Gibco 35050061), 10mM - HyClone™ HEPES Buffer (cytiva SH30237.01), 1X - Penicillin-Streptomycin (100X) (Sigma-Aldrich P0781), 0.1mM - 2-Mercaptoethanol (50 mM) (Gibco 31350010), 1000U.ml -  ESGRO® Recombinant Mouse LIF Protein 10^7 units/ml (Sigma-Aldrich ESG1107).","Sample Treatment - Differentiation Medium:  IMDM, GlutaMAX™ Supplement (Gibco 31980048), 15% - FBS (Capricorn Scientific FBS-12A, CP18-2152), 1X - Penicillin-Streptomycin (100X) (Sigma-Aldrich P0781), 0.1 mM - 2-Mercaptoethanol (50 mM) (Gibco 31350010), 50 µg/ml - L-Ascorbic acid (Sigma-Aldrich A5960-25G), 150 μg/mL -Transferrin (Roche 10652202001)","Sequencing - Illumina Novaseq 6000 is used for sequencing. With the manufacturer's recommended protocol has been followed. Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (CaG000338)","Nucleic Acid Extraction - The manufacturer's recommended protocol has been followed. Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (CaG000338)","Library Construction - The manufacturer's recommended protocol has been followed. Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (CaG000338)"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The raw data were processed with cellranger-arc-2.0.2 and mm10_CR_arc_v2.0.2 reference with manufacturer's recommendations.","Sequence Alignment - For scMultiome cellranger-arc-2.0.2 (manufacturer pipeline) used and reference genome mm10_CR_arc_v2.0.2.  For scRNAseq cellranger-7.2.0 (manufacturer pipeline) was used, and the transcriptome reference genome mm10-1.2.0."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"pubmed_abstract":["Hematopoiesis occurs in three consecutive overlapping waves in mammals, regulated by transcription factors. We investigated the role of three relatively poorly studied transcription factors in early embryonic hematopoietic development at single-cell resolution: Atf3, Zfp711 and Bcl6b. These transcription factors are upregulated early in development, when hematopoietic and endothelial lineages separate from cardiac and other mesodermal lineages. We combined multiplexed single-cell RNA sequencing and flow cytometric analysis with knockouts in in vitro differentiating mouse embryonic stem cells to dissect the function of these transcription factors in lineage specification. ΔAtf3 cells showed increased mesodermal differentiation but decreased endothelial cells and erythro-myeloid progenitors, accompanied by aberrant interferon signaling. Mechanistically, loss of Atf3 disrupted key hematopoietic regulatory genes (Runx1, Egr1, Jun, Fos, Mafb and Batf3) required for the formation of erythro-myeloid progenitors. ΔZfp711 cells exhibited increased blood progenitors and erythroid cells, but decreased endothelial cells, with a striking shift from Hoxa+ mesoderm (allantois and limb mesoderm) to Hoxb+ mesoderm (mesenchyme and epicardium). Notably, Zfp711 binds the Atf3 promoter, suggesting a hierarchical regulation. In contrast, ΔBcl6b had no observable effects on early hematopoiesis, despite specific expression in hemato-endothelial progenitors."],"study_type":["scATAC-seq"],"species":["Mus musculus"],"pubmed_title":["Distinct Roles of Atf3, Zfp711, and Bcl6b in Early Embryonic Hematopoietic and Endothelial Lineage Specification"],"pubmed_authors":["Ridvan Cetin","Ridvan Cetin,Giulia Picco,Jente van Staalduinen,Eric Bindels,Remco Hoogenboezem,Gregory van Beek,Mathijs A. Sanders,Yaren Fidan,Ahmet Korkmaz,Joost Gribnau,Jeffrey van Haren,Danny Huylebroeck,Eskeatnaf Mulugeta,Frank Grosveld"],"additional_accession":[]},"is_claimable":false,"name":"Single-Cell Multi-omics RNA and ATAC Sequencing of In Vitro Hematoendothelial Differentiation from Mouse Embryonic Stem Cells","description":"An in vitro differentiation system using mouse embryonic stem cells to capture multiple differentiation timepoints: days 3, 4, 5, 6, and 7 as scMultiome (ATAC+RNA) and days 0, 2, and 4 as scRNA-seq. scMultiome libraries were generated using the Single Cell Multiome ATAC + Gene Expression v1 chemistry, and scRNA-seq libraries were generated using the Single Cell 3' v3 chemistry. Nuclei isolation for scMultiome was performed using a modified 0.1X lysis protocol from 10x Genomics protocol CG000366, with the digitonin concentration adjusted from 0.001% to 0.005%.","dates":{"release":"2025-12-11T00:00:00Z","modification":"2026-04-15T14:00:33.367Z","creation":"2025-12-05T11:26:46.934Z"},"accession":"E-MTAB-16347","cross_references":{"pubmed":["41200855"],"ENA":["ERP186158"],"Biostudies":["E-MTAB-14678"],"EFO":["EFO_0002944","EFO_0004170","EFO_0010891","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"],"doi":["10.1242/dev.204792"]}}