{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Siddhant Kalra"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16209"],"description":["During differentiation of human airway basal stem cells, the confluent epithelium undergoes a phase transition from a fluid-like migratory unjammed phase to a solid-like stationary jammed phase. While mechanisms underlying this process, termed the jamming transition, remain poorly understood, here we demonstrate that the jamming transition coincides with the mesenchymal-to-epithelial transition (MET) during epithelial differentiation. Both the jamming transition and MET are delayed in airway basal stem cells cultured from asthmatic donors, a phenotype which can be recapitulated or abrogated through manipulation of TGF-β receptor activation."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - RNA sequencing was performed on a NovaSeq PE150. Library construction and sequencing was performed at the Oklahoma Medical Research Foundation Clinical Genomics Center.","Nucleic Acid Extraction - Total RNA was isolated from HBE cells frozen on ALI days 0, 1, 7, and 14 using the TRIzol Plus RNA Purification Kit (Invitrogen)","Library Construction - Sequencing libraries were constructed with a Watchmaker Genomics kit.","Sample Collection - Cells were grown according to the protocol in DOI 10.1385/1-59259-861-7:183 Passage 2 primary human bronchial epithelial (HBE) cells  were cultured in air-liquid interface (ALI) culture for up to 14 days in culture. HBE cells were grown normally according to the growth protocol above and frozen on ALI days 0, 1, 7, and 14 to allow for RNA extraction."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw count files from individual samples were merged into a single count matrix, which was then used to construct a DESeq2 object in R for differential expression analysis, using day as the design variable. Normalized expression values generated by DESeq2 were used to visualize gene expression dynamics over time","Sequence Alignment - Quality check of raw sequencing reads was conducted with the FastQC tool. To address high adaptor content, 91 base pairs were trimmed from the 3’ end of each read. Reads were then aligned to the human reference genome (Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using Bowtie2 with default parameters"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Concurrent control of airway basal stem cell differentiation transition and the mesenchymal-to-epithelial transition by the jamming"],"pubmed_authors":["Siddhant Kalra","Jennifer Mitchel","Jennifer A Mitchel, Jacob Notbohm, Reverie R Brown, Mikoto A Nakamura, Siddhant Kalra, Joseph D Coolon, Chimwemwe Mwase, Michael J O’Sullivan, and Jin-Ah Park"],"additional_accession":[]},"is_claimable":false,"name":"Concurrent jamming and mesenchymal-to-epithelial transitions during airway basal stem cell differentiation","description":"During differentiation of human airway basal stem cells, the confluent epithelium undergoes a phase transition from a fluid-like migratory unjammed phase to a solid-like stationary jammed phase. While mechanisms underlying this process, termed the jamming transition, remain poorly understood, here we demonstrate that the jamming transition coincides with the mesenchymal-to-epithelial transition (MET) during epithelial differentiation. Both the jamming transition and MET are delayed in airway basal stem cells cultured from asthmatic donors, a phenotype which can be recapitulated or abrogated through manipulation of TGF-β receptor activation.","dates":{"release":"2025-11-25T00:00:00Z","modification":"2025-11-25T17:54:02.989Z","creation":"2025-11-19T17:29:22.145Z"},"accession":"E-MTAB-16209","cross_references":{"ENA":["ERP185350"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}