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| Status |
Public on Jun 30, 2022 |
| Title |
Cas9 control scRNA-seq |
| Sample type |
SRA |
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| Source name |
mouse normal lung
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| Organism |
Mus musculus |
| Characteristics |
tissue: normal lung
eml4-alk adenovirus: No
gender: male
age at euthanize: 27 weeks
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| Treatment protocol |
all mice were injected with tamoxifen to label the specific cell types
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| Extracted molecule |
total RNA |
| Extraction protocol |
Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit V3.1
Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit V3.1
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Alignment: Cell Ranger 3.1
Normalization, QC: R 4.0.3, Seurat 3.2.2
Exclude bad quality cells among the samples: 1000-6000 for TAM, 1000-6000 for Cas9, 1000-6000 for 2 wk-1, 2000-6000 for 2 wk-2, 1500-6000 for 4 wk-1, 2000-6000 for 4-wk GFP+, 1000-6000 for tumour
Cells with more than 10% mitochondrial genes were removed
Normalization with a scaling factor of 10000
Genome_build: mm10
Supplementary_files_format_and_content: scaled_count_data: normalized count data per gene and per cell. Metadata cells: cell barcodes and their annotations in a tab-spearated dataset
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| Submission date |
Jun 04, 2021 |
| Last update date |
Jun 30, 2022 |
| Contact name |
Reka Toth |
| E-mail(s) |
r.toth@dkfz-heidelberg.de
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| Phone |
+496221424322
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| Organization name |
DKFZ
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| Street address |
Im Neuenheimer Feld 280
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| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE176185 |
Club cells employ regeneration mechanisms during lung tumorigenesis |
| GSE176186 |
Club cells employ regeneration mechanisms during lung tumorigenesis |
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| Relations |
| BioSample |
SAMN19572978 |
| SRA |
SRX11070918 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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