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Status |
Public on Jun 30, 2022 |
Title |
2 weeks timepoint, rep1 scRNA-seq |
Sample type |
SRA |
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Source name |
mouse lung, induced tumor
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Organism |
Mus musculus |
Characteristics |
tissue: lung, induced tumor eml4-alk adenovirus: Yes gender: female age at euthanize: 13 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 |
SAMN19572977 |
SRA |
SRX11070919 |
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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