{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Nadezhda Azbukina"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15622"],"description":["In order to systematically investigate, to which extent cell lines and experimental batches affect the consistency of organoid patterning, we conducted a multiplexed morphogen patterning experiment to study the reproducibility of the effects induced by retinoic acid, FGF-8, SHH and CHIR. We have tested influence of 2 neural induction methods, 2 experimental batches and 4 cell lines: H1 (XY), H9 (XX), WTC (XY) and WIBJ (XX) on cell type composition consistency after morphogen patterning using single-cell transcriptomic readout (Parse Bioscience) and pooling 3 organoids for each condition."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - After d21 in culture 3 organoids per condition per cell line were dissociated individually using CyBio FeliX liquid handler robot with thermoshaker. For dissociation we used a papain-based dissociation kit (Miltenyi Neural dissociation kit). Each organoid was dissociated using 410uL of enzyme mix 1 and 6uL of enzyme mix 2. Then single cell suspension from the same condition were pooled together (H1 and H9; WTC and WIBJ2).","Sequencing - Libraries were sequenced in S2 flowcell with Illumina Nova Seq technology, using paired-end 64/8/8/58 configuration.","Nucleic Acid Extraction - Each individual single cell suspension has been followed by  fixation and  permeabilization procedures, which were performed according to the manufacturer specification (ParseBiosciences, cell fixation kit v3, CF100).","Library Construction - Collected samples were processed for highly multiplexed single-cell RNA sequencing (scRNA-seq) using a split-pool combinatorial barcoding kit (ParseBiosciences, WT Mega kit v3, MG100)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Transcript counts were normalized to the total number of counts for that cell, multiplied by a scaling factor of 10,000 and subsequently natural-log transformed. We used scanpy python package (v1.10.3).","Sequence Alignment - We used Parse Biosciences Software (v1.3.1) to demultiplex barcodes, map to hg38 human transcriptome and generate count matrix."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Nadezhda Azbukina","Fátima Sanchís Calleja"],"additional_accession":[]},"is_claimable":false,"name":"scRNA-seq of human neural brain organoids patterning reproducibility screening","description":"In order to systematically investigate, to which extent cell lines and experimental batches affect the consistency of organoid patterning, we conducted a multiplexed morphogen patterning experiment to study the reproducibility of the effects induced by retinoic acid, FGF-8, SHH and CHIR. We have tested influence of 2 neural induction methods, 2 experimental batches and 4 cell lines: H1 (XY), H9 (XX), WTC (XY) and WIBJ (XX) on cell type composition consistency after morphogen patterning using single-cell transcriptomic readout (Parse Bioscience) and pooling 3 organoids for each condition.","dates":{"release":"2025-10-01T00:00:00Z","modification":"2026-05-27T12:16:28.418Z","creation":"2025-09-23T12:01:48.657Z"},"accession":"E-MTAB-15622","cross_references":{"ENA":["ERP180513"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}