{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Masahito Yoshihara"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13992"],"description":["PAX6-EGFP, TP63-tdTomato reporter iPSCs were cultured using the self-formed ectodermal autonomous multi-zone (SEAM) method (Hayashi et al, Nature 2016) for 10 weeks to generate ocular surface epithelial cell sheets. These epithelial cells were isolated and defined as EGFP-/tdTomato+ (P1), EGFPlow/tdTomato+ (P2), EGFPmid/tdTomato+ (P3), and EGFPhigh/tdTomato+ (P4)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Sorted hiPSCs were plated onto iMatrix511silk-coated (0.5 μg/cm2) cell culture inserts. The cells were cultured in OEM (DMEM/F12 containing 10 μM Y-27632, 2% B27 supplement, 1% penicillin-streptomycin solution, and 10ng/m of KGF) at 37 °C until confluence (4 weeks).","Nucleic Acid Extraction - Total RNA was purified using an RNeasy Micro Kit with RNase-free DNase (both from Qiagen, Hilden, Germany).","Sequencing - The libraries were quantified using Q-PCR, immobilized, and processed onto a flow cell using a cBot device (Illumina), and then subjected to sequencing-by-synthesis using a NovaSeq 6000 S4 chemistry device on a NovaSeq 6000 platform at Macrogen (Tokyo, Japan).","Library Construction - RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina), and the quality and quantity of the amplicons were assessed at all steps through capillary electrophoresis (Agilent Bioanalyzer and TapeStation; Agilent, Santa Clara, CA, USA)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Read counts were quantified using the rsemcalculated expression function in RSEM (version 1.3.3). The resulting transcripts per million values were used to generate heatmaps."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Masahito Yoshihara","Rei Kamuro"],"additional_accession":[]},"is_claimable":false,"name":"Characterization of human iPSC-derived ocular surface epithelial cell sheets depending on PAX6 gene expression levels","description":"PAX6-EGFP, TP63-tdTomato reporter iPSCs were cultured using the self-formed ectodermal autonomous multi-zone (SEAM) method (Hayashi et al, Nature 2016) for 10 weeks to generate ocular surface epithelial cell sheets. These epithelial cells were isolated and defined as EGFP-/tdTomato+ (P1), EGFPlow/tdTomato+ (P2), EGFPmid/tdTomato+ (P3), and EGFPhigh/tdTomato+ (P4).","dates":{"release":"2025-07-31T00:00:00Z","modification":"2025-08-01T00:01:33.649Z","creation":"2024-04-09T10:28:37.713Z"},"accession":"E-MTAB-13992","cross_references":{"ENA":["ERP159295"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}