{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":[null],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15075"],"description":["Single-cell sequencing of floor plate-like cells from synNotch co-cultures expressing Sonic Hedgehog"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - The PIPseq manufacturer's guide was then followed for library preparation.","Sample Collection - Cells were lifted using Accutase and spun down at 300xg for 5 minutes before being resuspended in PBS (w/o calcium or magnesium).","Nucleic Acid Extraction - Cells were encapsulated using the PIPseq method. The PIPseq manufacturer's guide was then followed for nucleic acid extraction. The PIPseq T2 kit v3 chemistry was used.","Sequencing - Reads were generated from an Illumina NovaSeq6000 (S4) PE150 sequencing run.","Growth Protocol - H9 hESCs were plated at a density of 400,000 cells/cm2 in 96-well plates coated with Geltrex. SynNotch conditions were seeded at 1:1 ratio of senders:receivers. Neural induction medium was prepared on day 0 and contained neurobasal medium (Gibco, 21103049) supplemented with 1% N2 supplement (Gibco, 17502048), 2% B-27 supplement without vitamin A (Gibco, 12587010), 1% GlutaMAX (Gibco, 35050061), 10 μM SB431542 (STEMCELL TECH, 72234), 100 nM LDN193189 (STEMCELL TECH, 72149), and 10 μM Y-27632. WT H9 hESCs were also plated with 200 ng/mL SHH protein (Sonic C25II, R&D Systems, 464-SH). Medium was prepared (excluding Y-27632) and changed daily, and cells were taken out to 11 days in culture."],"figure_sub":["MINSEQE Score","Assays and Data","Processed Data","organisation","MAGE-TAB Files"],"data_protocol":["Data Transformation - Cells containing between 1600 and 7500 were retained. All data were merged, normalized, scaled based on the top 2000 variable features, and then scored for cell cycle using the default implementation in Seurat. Data were visualized using principal component analysis and uniform manifold approximation and projection.","Sequence Alignment - Reads were aligned using the pipseeker algorithm at a resolution of 5 and then read into Seurat (v5)."],"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_title":["Induced neural progenitor specification from human pluripotent stem cells by a refined synthetic Notch platform"],"additional_accession":["ERP171898"],"pubmed_authors":["Catherine Hamann","Catherine A. Hamann, Andrew Kjar, Hyosung Kim, Alan J. Simmons, Hannah J. Brien, Cheryl I. Quartey, Bonnie L. Walton, Ken S. Lau, Ethan S. Lippmann, and Jonathan M. Brunger"]},"is_claimable":false,"name":"Single cell analysis of SHH-patterned hESCs","description":"Single-cell sequencing of floor plate-like cells from synNotch co-cultures expressing Sonic Hedgehog","dates":{"release":"2025-05-08T00:00:00Z","modification":"2026-05-27T14:38:28.138Z","creation":"2025-04-23T14:28:21.75Z"},"accession":"E-MTAB-15075","cross_references":{"ENA":["ERP171898"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}