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Series GSE215895 Query DataSets for GSE215895
Status Public on Jan 17, 2023
Title A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung [SC]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The lung contains numerous specialized cell-types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a comprehensive topographic atlas of early human lung development. Here, we report 83 cell states, several spatially-resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated scRNA-Seq and spatially resolved transcriptomics into a web-based, open platform for interactive exploration. We show distinct gene expression programs, accompanying sequential events of cell differentiation and maturation of the secretory and neuroendocrine cell-types in proximal epithelium. We define the origin of airway fibroblasts associated with airway smooth muscle in bronchovascular bundles and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases.
Overall design For tissue dissociation, tracheas were removed and lungs were finely minced. For later timepoints, lobes were first dissected into smaller pieces. Then, they were digested in 4U/ml Elastase (Worthington, cat no. LS002292), 1 mg/ml of DNase (Worthington, cat no. LK003170) in HBSS (Gibco, cat no. 14170) at 37°C ranging between 30 min to 3 h depending on the age (older timepoints require longer digestion times). HBSS supplemented with 2 % FCS (Gibco, cat no. 10500064) was used for the whole procedure. The tissues were triturated with fire polished glass Pasteur pipettes every 15-20 min for the tissue to fall apart more easily and enhance the dissociation. After digestion, the cell suspension was filtered (twice if needed) in a 15ml Falcon tube using a 30μm cell strainer (CellTrics, Sysmex), to remove remaining undissociated clumps and debris. The filtered cell suspension was kept ice cold and was diluted (roughly 1:2) with ice cold HBSS to prevent further digestion by the enzyme.. The filtered cell suspension wascells were pelleted through centrifugation at 200g for 5 min at 4 °C, the supernatant was removed and the pellet resuspended in a small volume of calcium- and magnesium-free HBSS (Gibco, cat no.14170) and transferred to 1.5ml Eppendorf tubes precoated with 30% BSA (A9576, Sigma-Aldrich). A Bürker chamber was used for cell counting.
NOTE FROM SUBMITTER: raw reads from our cohort are considered sensate and protected by GDPR regulations, and will therefore be uploaded to Swedish federated EGA.
Contributor(s) Sergio MS, Alexandros S, Paulo C, Christos S
Citation(s) 36646791
Submission date Oct 17, 2022
Last update date Jan 20, 2023
Contact name Paulo Czarnewski
Organization name KTH
Street address Tomtebodavägen 23b
City Solna
ZIP/Postal code 171 65
Country Sweden
Platforms (1)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (39)
GSM6645126 lung,PCW8.5, rep1 [10X140w1]
GSM6645127 lung,PCW6, rep1 [10X151w1]
GSM6645128 lung,PCW8, rep1 [10X158w3]
This SubSeries is part of SuperSeries:
GSE215898 A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung
BioProject PRJNA891256

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE215895_RAW.tar 1.4 Gb (http)(custom) TAR (of H5)
Processed data provided as supplementary file
Raw data not provided for this record

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