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| Status |
Public on Apr 18, 2024 |
| Title |
All samples |
| Sample type |
SRA |
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| Source name |
Lung
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| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
time: day 0, 7, 14, 21
cell type: Mesenchymal cells
genotype: Scube-CreER +/+, Rosa26 tdTomato/tdTomato
treatment: non-bleomycin-treated or bleomycin treated
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| Treatment protocol |
Sucbe2-CreER/Rosa26-tdTomato double homozygous mice were treated with 2mg tamoxifen/day for two weeks. Two weeks after the last tamoxifen injection, mice were treated with 2.5U/kg bleomycin by oropharyngeal aspiration, and harvested on day 0 (non-bleomycin treated), 7, 14, and 21
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| Extracted molecule |
total RNA |
| Extraction protocol |
Lungs were harvested and dissociated by collagenase and dispase at 37C for 60 min. Mesenchymal cells (CD31-, CD45-, EpCAM-, Ter119-) were enriched by magnetic negative selection and FACS.
Three biological replicates at each time point were multiplexed by 10x Genomics 3’ CellPlex Kit. Tag assignment was as follows; day 0 (301, 302, 303), day 7 (304, 305, 306), day 14 (307, 308, 309), and day 21 (310, 311, 312). All 12 samples were pooled and 30,000 cells / lane were loaded onto 4 lanes of Chromium Next GEM Chip (10x Genomics). Chromium Single Cell 3’ v3.1 (10x Genomics) reagents were used for library preparation
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Fastq files were uploaded to 10x Genomics cloud analysis website (https://www.10xgenomics.com/products/cloud-analysis) and reads were aligned to a custom reference of mouse genome mm10 with tdTomato-WPRE-polyA transcript sequence.
The data were demultiplexed and multiplets identified by the presence of multiple oligonucleotide tags were removed using 10x Genomics cloud analysis function with default parameters.
Raw count matrices were imported to the R package Seurat v4.1.0 and cells with fewer than 200 detected genes, larger than 7500 detected genes, or larger than 15% percent mitochondria genes were excluded.
We used DoubletFinder package for individual samples to remove doublets that were not detected upon alignment using estimated multiple rate 2%.
We then merged all the sample objects by RunFastMNN
Assembly: mm10 with tdTomato-WPRE-polyA
Supplementary files format and content: rds file: Seurat v4 object after filtering, merging, and clustring
Supplementary files format and content: mtx, tsv, csv files: raw count, barcode, genes, and meta data before any filtering
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| Submission date |
Aug 02, 2022 |
| Last update date |
Apr 18, 2024 |
| Contact name |
Tatsuya Tsukui |
| E-mail(s) |
tatsuya.tsukui@ucsf.edu
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| Organization name |
UCSF
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| Department |
Medicine
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| Street address |
555 Mission Bay Blvd South, 282
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE210341 |
Single-Cell RNA-sequencing of lung mesenchymal cells at multiple time points after bleomycin injury |
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| Relations |
| BioSample |
SAMN30105858 |
| SRA |
SRX16774159 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6428697_barcodes.tsv.gz |
226.9 Kb |
(ftp)(http) |
TSV |
| GSM6428697_genes.tsv.gz |
205.4 Kb |
(ftp)(http) |
TSV |
| GSM6428697_matrix.mtx.gz |
516.2 Mb |
(ftp)(http) |
MTX |
| GSM6428697_metadata.csv.gz |
624.2 Kb |
(ftp)(http) |
CSV |
| GSM6428697_seurat_v4_obj.rds.gz |
1.4 Gb |
(ftp)(http) |
RDS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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