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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 30, 2022 |
| Title |
MsCCSP_tumor02 |
| Sample type |
SRA |
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| Source name |
Scgb1a1 lineage tumor
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| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
group: tumor
eml4-alk adenovirus: Yes
gender: female
characteristics: age by euthanize: 31, 36 and 36 weeks
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| Treatment protocol |
DNA was extracted using the QIAamp DNA micro Kit
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
all mice were injected with tamoxifen to label the specific cell types
According to Wang et al Nat Protoc. 2013 Oct;8(10):2022-32.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Alignment: methylCtools 1.0 (BWA Version 0.7.8 -T 0 Merging Sambamba Version 0.6.5 -t 1 -l 0 --hash-table-size=2000000 --overflow-list-size=1000000 --io-buffer-size=64 Samtools Version 0.1.19)
methylation calling: MethylDackel --nOB 2,11,11,2 --nOT 8,1,2,11.
Processing: R 4.0.2, Methrix
Excluded non-covered sites,
Excluded SNP overlapping sites,
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files: chr, start position, end position, methylation beta value
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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 |
GPL13112 |
| Series (2) |
| GSE176184 |
Club cells employ regeneration mechanisms during lung tumorigenesis |
| GSE176186 |
Club cells employ regeneration mechanisms during lung tumorigenesis |
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| Relations |
| BioSample |
SAMN19572991 |
| SRA |
SRX11070825 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5359543_MsCCSP_tumor02.bedGraph.gz |
136.3 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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