{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Elisa Balmas"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15693"],"description":["Summary Single-cell RNA sequencing was performed on cardiac organoids differentiated from WTC11 hiPSCs (TTN-mEGFP) to investigate chamber-specific lineage commitment. Organoids were collected at day 7.5 of differentiation, using protocols designed to direct progenitors toward left ventricle, right ventricle, or atrium fates. This dataset enables the characterization of transcriptional programs and cellular heterogeneity underlying the early specification of the cardiac chamber.  Dataset: This dataset contains single-cell RNA sequencing (scRNA-seq) data generated to compare the development of cardiac organoids differentiated from WTC11 hiPSCs (TTN-mEGFP reporter line). Organoids were harvested at day 7.5 of differentiation, a stage at which chamber-specific programs begin to emerge.  Each sample corresponds to a distinct differentiation protocol designed to direct the commitment of progenitors toward a specific cardiac chamber identity: the left ventricle, the right ventricle, or the atrium. The experimental rationale, illustrated in Supplementary Figure 4 (Figure S4) of Becca et al. (2025), highlights the use of scRNA-seq to resolve the cellular heterogeneity of these chamber-directed organoids and to define transcriptional signatures associated with early cardiac chamber specification."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - 10X genomics technology with CG000388 Rev B (with cell multiplexing oligos). Cells were loaded on a chip G.","Library Construction - the single cell library was created with CG000388 Rev B (with cell multiplexing oligos).","Sample Collection - Digestion with versene and trippleE. Then cells were labeled with CMO, and sorted for vital cells and then loaded on the 10X controller. We processed the organoids with trypsin and obtained a single-cell suspension. We then labeled the cells with cell multiplexing oligos (CMO) before loading on a reaction of 3' Next GEM single cellv3.1 kit.  Cells were washed with PBS and 1% BSA (Miltenyi) and then labeled with CMOs following the 10x Genomics protocol (CG000391 RevA). After three washes with PBS and 1% BSA, cells were incubated for 15 minutes at room temperature with Fixable Viability Dye eFluor™ 780 (Invitrogen 1:1000 dilution). Cells were washed again and sorted with a SONY SH800S sorter with a 100 µm chip in FACS tubes, then pooled together in equal quantities, and resuspended at 1,600 cells/µL to be loaded on the 10X chromium with a target of 16,000 cells per reaction.","Sequencing - Cell multiplexing barcodes were pulled in molar ratio compared to the gen expression library 1:6 and libraries were loaded on 3 lanes of a Novaseq 6000 with standard 10X 3' sequencing parameters reported in the userguide (R1=28, indexes=10, R2=90)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Data provided are row. Use the atached aggregation.csv and config_multi.csv files to run cell ranger aggr (aggregation.csv) and then cell ranger multi (config_multi.csv)","Data Transformation - an RData file is atached with the full processed data (cds_filtered_all.RData and cds_joined.RData which include all dataset together). Data can be read in R or in Rstudio and then it can be read and used with monocle 3. Additional R files with data annotation (seurat_meta_norm.RData and meta_cluster_transfering.RData with cds_joined annotations and cluster transfering between datasets) and counts data (seurat_filtered2.RData) are  provided to be analyzed with different platforms. Additionally, the output of this pipeline filtered_feature_bc_matrix files (barcodes.tsv.gz and features.tsv.gz) is also provided to allow independent filtering and analysis."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Sara Bianchi","Elisa Balmas"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell RNA sequencing of hiPSC-derived cardiac organoids patterned toward chamber-specific fates (left ventricle, right ventricle, atrium)","description":"Summary Single-cell RNA sequencing was performed on cardiac organoids differentiated from WTC11 hiPSCs (TTN-mEGFP) to investigate chamber-specific lineage commitment. Organoids were collected at day 7.5 of differentiation, using protocols designed to direct progenitors toward left ventricle, right ventricle, or atrium fates. This dataset enables the characterization of transcriptional programs and cellular heterogeneity underlying the early specification of the cardiac chamber.  Dataset: This dataset contains single-cell RNA sequencing (scRNA-seq) data generated to compare the development of cardiac organoids differentiated from WTC11 hiPSCs (TTN-mEGFP reporter line). Organoids were harvested at day 7.5 of differentiation, a stage at which chamber-specific programs begin to emerge.  Each sample corresponds to a distinct differentiation protocol designed to direct the commitment of progenitors toward a specific cardiac chamber identity: the left ventricle, the right ventricle, or the atrium. The experimental rationale, illustrated in Supplementary Figure 4 (Figure S4) of Becca et al. (2025), highlights the use of scRNA-seq to resolve the cellular heterogeneity of these chamber-directed organoids and to define transcriptional signatures associated with early cardiac chamber specification.","dates":{"release":"2025-10-14T00:00:00Z","modification":"2026-05-27T12:50:43.118Z","creation":"2025-10-10T13:01:02.068Z"},"accession":"E-MTAB-15693","cross_references":{"ENA":["ERP181353"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}