biostudies-arrayexpressCarlos Sainz-ZuñigaHomo sapiensPythonhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15033HiPSCs 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. Raw data contains 8 sublibraries which include hiPSC-derived passage 2 (day 76) AT2 cells.(at2_ep_filt_4_3).biostudies-arrayexpressSample 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.Library Construction - Single-cell RNA-seq libraries were generated using the Evercode WT v2.3 kit (Parse Biosciences). 8 sublibraries were generated.Sequencing - Libraries were sequenced at 4 billion total reads, and at 40,000 reads per cell.Nucleic Acid Extraction - Nucleic acid extraction was obtained following Evercode WT v2.3 Parse Biosciences protocol. RT transcription was performed within each cell following single cell combinatorial barcoding. Following barcoding, cells were lysed and nucleic acid molecules extracted.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw sequence reads were aligned using Parse Bioscience Pipeline. Mapping was done against the human genome GRCh38.p14. An unfiltered count matrix was used for further processing using scanpy in Python V3.12. Cells and genes with low complexity were filtered out (fewer than 100 expressed genes, and genes expressed in less than 5 cells). Cells with high mitochondrial percentage content were removed (threshold set at <50%). Genes per Unique Molecular Identifier (UMI) was used as a parameter to filter out cells with high levels of reads and filter out outliers. (threshold set at <65%). Cells were log normalised set to 10,000 cells as scale.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XRNA-seq of coding RNA from single cellsHomo sapiensCarlos Sainz-ZuñigaAna Serna-ValverdeNicholas HannanLiam ReedfalseSingle-cell sequencing samples for chemically defined, serum-free, and xeno-free differentiation of alveolar type 2 cellsHiPSCs 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. Raw data contains 8 sublibraries which include hiPSC-derived passage 2 (day 76) AT2 cells.(at2_ep_filt_4_3).2026-04-01T00:00:00Z2026-04-02T01:04:57.708Z2025-04-15T13:06:12.725ZE-MTAB-15033ERP171653E-MTAB-15034EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0003816EFO_0004184