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| 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
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| 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.
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| 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.
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| 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 |
| E-mail(s) |
czarnewski@gmail.com
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| Organization name |
KTH
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| Street address |
Tomtebodavägen 23b
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| City |
Solna |
| ZIP/Postal code |
171 65 |
| Country |
Sweden |
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| Platforms (1) |
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| Samples (39)
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| GSM6645129 |
lung,PCW8.5, rep2 [10X166w2] |
| GSM6645130 |
lung,PCW5, rep1 [10X180w1] |
| GSM6645131 |
lung,PCW12, rep1 [10X189w1] |
| GSM6645132 |
lung,PCW12, rep2 [10X189w2] |
| GSM6645133 |
lung,PCW13, rep1 [10X214w1] |
| GSM6645134 |
lung,PCW13, rep2 [10X214w2] |
| GSM6645135 |
lung,PCW13, rep3 [10X247w1] |
| GSM6645136 |
lung,PCW13, rep4 [10X247w2] |
| GSM6645137 |
lung,PCW13, rep5 [10X247w3] |
| GSM6645138 |
lung,PCW13, rep6 [10X247w4] |
| GSM6645139 |
lung,PCW14, rep1 [10X253w3] |
| GSM6645140 |
lung,PCW14, rep2 [10X253w4] |
| GSM6645141 |
lung,PCW14, rep3 [10X253w5] |
| GSM6645142 |
lung,PCW14, rep4 [10X253w6] |
| GSM6645143 |
lung,PCW14, rep5 [10X253w7] |
| GSM6645144 |
lung,PCW14, rep6 [10X253w8] |
| GSM6645145 |
lung,PCW14, rep7 [10X256w1] |
| GSM6645146 |
lung,PCW12, rep1 [10X263w1] |
| GSM6645147 |
lung,PCW12, rep2 [10X263w2] |
| GSM6645148 |
lung,PCW12, rep3 [10X263w3] |
| GSM6645149 |
lung,PCW11.5, rep1 [10X272w1] |
| GSM6645150 |
lung,PCW11.5, rep2 [10X272w2] |
| GSM6645151 |
lung,PCW11.5, rep3 [10X272w3] |
| GSM6645152 |
lung,PCW11.5, rep4 [10X272w4] |
| GSM6645153 |
lung,PCW11.5, rep5 [10X274w2] |
| GSM6645154 |
lung,PCW11.5, rep6 [10X274w3] |
| GSM6645155 |
lung,PCW10, rep1 [10x285w3] |
| GSM6645156 |
lung,PCW10, rep2 [10x285w4] |
| GSM6645157 |
lung,PCW6, rep2 [10x289w3] |
| GSM6645158 |
lung,PCW6, rep3 [10x289w4] |
| GSM6645159 |
lung,PCW7, rep1 [10x299w3] |
| GSM6645160 |
lung,PCW7, rep2 [10x299w4] |
| GSM6645161 |
lung,PCW7, rep3 [10x299w5] |
| GSM6645162 |
lung,PCW7, rep4 [10x299w6] |
| GSM6645163 |
lung,PCW5.5, rep2 [10x303w3] |
| GSM6645164 |
lung,PCW5.5, rep1 [10x303w4] |
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| This SubSeries is part of SuperSeries: |
| GSE215898 |
A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung |
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| Relations |
| BioProject |
PRJNA891256 |
| 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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