{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Carlos Sainz-Zuñiga"],"organism":["Homo sapiens"],"software":["R"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15034"],"description":["HiPSCs were differentiated into alveolar type 2 cells (AT2s) following a stepwise differentiation protocol, mimicking lung development, using a chemically defined, serum-free, and xeno-free differentiation protocol. Samples contain biological triplicates of each developmental stage (hiPSCs, definitive endoderm, lung progenitor stage, passage 0 AT2s, early and late passage AT2s) using the same cell line. Additionally, a biological triplicate for a cell line from an idiopathic pulmonary fibrosis patient with a homozygous surfactant protein C mutation was done for late-passage AT2s comparison."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - For dissociation, spheroids were collected and centrifuged at 200g for 4 minutes and resuspended in a dissociation mix of  0.125 mg/mL Collagenase (Merck, C9891), 1 U/mL Dispase II (Thermo Fisher Scientific, #17105041) and 0.1 U/μL DNase (Merck, D4527) mixed in DMEM/F12 (Dulbecco’s Modified Eagle’s Media: Nutrient Mixture F-12; Thermo Fisher Scientific, #11330-057) for 20 minutes at 37°C on a DLAB MX-T6-Pro Roller at 10 RPM. Dissociation mix was neutralised using 1:3 dilution with basal media and centrifuged at 200 RCF for 5 minutes. Spheroids were resuspended in dissociation mix consisting of 0.05% trypsin-EDTA (Gibco, #25300062) and 0.1 U/μL DNase and placed at 37°C for 10-15 minutes, resuspending manually every 3 minutes. Dissociation mix was neutralised using 10% foetal bovine serum solution in DMEM/F12 at 1:3 dilution. Cells were centrifuged at 300 RCF for 5 minutes, and then counted.","Nucleic Acid Extraction - RNA extraction was done following RNeasy Mini kit (Qiagen, #74106) instructions.","Sequencing - Samples were outsourced to GENEWIZ for sequencing of samples at 30 million reads, as 150 base paired end reads, and alignment to reference genome **GRCh38 p7**.","Library Construction - Samples were outsourced to GENEWIZ for nucleic acid library construction, and processed for ribosomal RNA depletion, and library preparation using standard NEB kit from New England Biolabs."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Bioinformatic analysis was done using RStudio. The limma package from Bioconductor was used to statistically analyse bulk mRNA expression dataset. Data was normalised using variance stabilizing transformation (vst). Normalised gene count dataset was tested for differential gene expression using limma to fit linear models. Empirical Bayes moderation of the standards errors towards a common value were done between samples for differential expression analysis, using a threshold p-value of 0.05. Benjamini-Hochberg procedure (False Discovery Rate) was used to multiple hypothesis test correction and was used as the adjusted p-value for gene differential expression analysis."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Carlos Sainz-Zuñiga","Ana Serna-Valverde","Nicholas Hannan","Liam Reed"],"additional_accession":[]},"is_claimable":false,"name":"Chemically defined, serum-free and xeno-free generation of mature type 2 alveolar epithelial cells from hiPSCs","description":"HiPSCs were differentiated into alveolar type 2 cells (AT2s) following a stepwise differentiation protocol, mimicking lung development, using a chemically defined, serum-free, and xeno-free differentiation protocol. Samples contain biological triplicates of each developmental stage (hiPSCs, definitive endoderm, lung progenitor stage, passage 0 AT2s, early and late passage AT2s) using the same cell line. Additionally, a biological triplicate for a cell line from an idiopathic pulmonary fibrosis patient with a homozygous surfactant protein C mutation was done for late-passage AT2s comparison.","dates":{"release":"2026-04-01T00:00:00Z","modification":"2026-04-02T01:05:01.251Z","creation":"2025-04-15T13:13:30.887Z"},"accession":"E-MTAB-15034","cross_references":{"ENA":["ERP171654"],"Biostudies":["E-MTAB-15033"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}