biostudies-arrayexpressXiangning DongHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17234Lung basal cells were isolated from human trachea and cultured in airway organoid media with and without the addition of RSPO1. After establishment airway organoids RSPO1 was added for two weeks of culture. Data is from two distinct primary airway organoid lines and performed single nucleus-RNA sequencing.biostudies-arrayexpressSample Collection - Human lung tissue research was reviewed and approved by The University of Michigan Institutional Review Board (IRB). Normal, de-identified human fetal lung tissue was obtained from the University of Washington Laboratory of Developmental Biology. Specific tissue regions were dissected according to anatomic region and airway organoids were established from Trachea micro dissections. After establishment Airway Organoids were either kept as control, or treated with 5% RSPO1 conditioned media for 14 days. Samples were flash frozen for nuclei isolation.Nucleic Acid Extraction - Nuclei were isolated from the samples using the standard protocol for the 10X Chromium Nuclei Isolation Kit(10X Cat#1000437) by the authors. Nuclei were submitted to the University of Michigan Advanced Genomics Core for 10X On-Chip Multiplexing (OCM).Library Construction - Single-cell suspensions from two control Airway Organoid lines and their RSPO1 treated cognates were multiplexed using 10x Genomics Chromium On-Chip Multiplexing (OCM) and processed together as a single Chromium Gene Expression v4 library. Following OCM labeling, cells from all specimens were pooled prior to GEM generation and library construction according to the manufacturer’s protocol. Because multiplexing occurred before library generation, a single sequencing library and corresponding raw FASTQ files were produced for the pooled sample.Sequencing - All RNA-sequencing was performed using Illumina Novaseq 6000 by the University of Michigan Advanced Genomics Sequencing Core.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw sequencing reads were processed using Cell Ranger Multi (10x Genomics). OCM barcode information (cells_per_tag.json) was used to assign individual cell barcodes to their originating biological specimens. Cell-level sample assignments were generated for specimens. Raw FASTQ files correspond to the pooled library, whereas specimen-specific count matrices and metadata were generated after demultiplexing and are provided as processed data files (filtered_feature_bc_matrix.h5). Ambient background removal was performed by Cellbender v03 to produce a background corrected matrix for each sample (output_filtered.h5).UnknownTranscriptomicsN/AChromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle,Illumina NovaSeq 600010X Genomics reagent kit<h4>ABSTRACT</h4> Organs are composed of diverse cell types that change across space and time during development. To interrogate this diversity, we micro-dissected developing human lungs along the proximal-distal axis during the late pseudoglandular stage and generated an integrated analysis of single-nucleus sequencing and spatial transcriptomics, creating a cellularly-resolved atlas of the lung. These rich datasets revealed positional niches and cellular heterogeneity along the proximal-distal axis, including the identification of a unique population of TP63 + basal cells, the primary stem cell of the airway, marked by expression of LGR5 and LGR6 . Analysis of the LGR5+ basal cell niche and functional experiments with primary organoid models suggest a tonic level of WNT pathway activity in LGR5 + basal cells that is potentiated by mesenchyme-derived R-SPONDIN. We found that basal cell self-renewal is enhanced by WNT activity, suggesting that the WNT pathway plays a previously unappreciated but critical role in airway stem cell maintenance during human development. These results enhance our fundamental understanding of the positional and cellular heterogeneity in the developing human lungs and begin to reveal unique niches that maintain homeostasis throughout the lung.single nucleus RNA sequencingHomo sapiensA spatially-resolved blueprint of the developing human lung reveals a WNT-driven niche for basal stem cellsXiangning DongTristan FrumPeggy HsuPeggy P. Hsu, Ansley S. Conchola, Tristan Frum, Xiangning Dong, Lila Tudrick, Varun Ponnusamy, Michael S. Downey, Manqi Wu, Mengkun Yang, Yusoo Lee, Emma Niestroy, Yu-Hwai Tsai, Angeline Wu, Sha Huang, Ian A. Glass, Sofia D. Merajver, and Jason R. SpenceJason SpencefalseIn vitro regulation of human basal cell subtypes through the WNT signaling pathwaysLung basal cells were isolated from human trachea and cultured in airway organoid media with and without the addition of RSPO1. After establishment airway organoids RSPO1 was added for two weeks of culture. Data is from two distinct primary airway organoid lines and performed single nucleus-RNA sequencing.2026-05-29T00:00:00Z2026-06-25T16:28:01.026Z2026-06-25T16:27:41.058ZE-MTAB-17234ERP195737EFO_0002944EFO_0004170EFO_0009809EFO_0005518EFO_0003816EFO_000418410.1101/2024.10.01.612096