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| Status |
Public on Aug 03, 2020 |
| Title |
Day28_AT2_Tomato |
| Sample type |
SRA |
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| Source name |
Lineage labelled AT2 cells were collected at day 28 post injury
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| Organism |
Mus musculus |
| Characteristics |
cell type: lung progenitor cells
strain: C57BL/6
tissue: Lung
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| Treatment protocol |
IL-1β or PBS were treated for organoid culture.
0.2mg/g body weight tamoxifen was given via intraperitoneal (IP) injection.
1.25U/kg of bleomycin, or PBS control, were delivered intratracheally.
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| Growth protocol |
Lung organoids were co-culutured with stromal cells.
Mice for the lineage tracing and injury experiments were bred and maintained under specific-pathogen-free conditions at the Cambridge Stem Cell Institute and Gurdon Institute of University of Cambridge.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Established organoids of control or IL-1β-treatment were incubated with dispase (BD Bioscience) for 30-60min. Then, cells were dissociated with TripLE for 5min, followed by washing with buffer (PBS/0.01% BSA).
For SPC or Krt8 lineage-labelled cells, CD45–CD31–EpCAM+Tomato+ cells were sorted at specific time points (at day 14 and day 28 post damage) from PBS or Bleomycin-treated mice (2 mice were pooled for each experiment). For non-lineage-labelled cells isolated from SPCCreERT2;R26RtdTomato mice in parallel with experiment of SPC lineage-labelled cells, we combined the cells of EpCAM+Tomato– and EpCAM– population with a ratio of 2:1, respectively.
The resulting cell suspension (~110,000 cells each) were submitted as separate samples to be barcoded for the droplet-encapsulation single- cell RNA-seq experiments using the Chromium Controller (10X Genomics). Single cell cDNA synthesis, amplification and sequencing libraries were generated using the Single Cell 3' Reagent Kit as per the 10x Genomics protocol.
10x libraries were multiplexed so that 2 libraries were sequenced per single lane of HiSeq 4000
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Droplet-based sequencing data was aligned and quantified using the Cell Ranger Single-Cell Software Suite (version 2.0.2, 10x Genomics Inc) using the Mus musculus genome (mm9,GRCm38) (official Cell Ranger reference, version 1.2.0). Cells were filtered by custom cutoff (more than 500 and less than 7000 detected genes, more than 2000 UMI count) to remove potential empty droplets and doublets.
Downstream analysis included data normalisation, highly variable gene detection, log transformation, principal component analysis, neighbourhood graph generation and Louvain graph-based clustering, which was done by python package scanpy (version 1.3.6) using default parameters.
Genome_build: Mus musculus, mm9/GRCm38
Supplementary_files_format_and_content: raw fastq files and raw gene quantifications, mtx/tsv format for matrix, barcode, and genes
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| Submission date |
Feb 10, 2020 |
| Last update date |
Aug 04, 2020 |
| Contact name |
Joo-Hyeon Lee |
| Organization name |
Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge
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| Street address |
Puddicombe Way, Cambridge Biomedical Campus
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| City |
Cambridge |
| ZIP/Postal code |
CB2 0AW |
| Country |
United Kingdom |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE144553 |
Inflammatory Signals induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration |
| GSE145031 |
Inflammatory Signals induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration |
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| Relations |
| BioSample |
SAMN14078564 |
| SRA |
SRX7703157 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4304613_Day28_AT2_Tomato.mtx.gz |
48.9 Mb |
(ftp)(http) |
MTX |
| GSM4304613_Day28_AT2_Tomato_barcodes.tsv.gz |
2.2 Mb |
(ftp)(http) |
TSV |
| GSM4304613_Day28_AT2_Tomato_gene.tsv.gz |
212.7 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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