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Sample GSM6938407 Query DataSets for GSM6938407
Status Public on Jun 30, 2023
Title X2.non
Sample type SRA
 
Source name Lung
Organism Homo sapiens
Characteristics tissue: Lung
cell line: SAEC
cell type: human normal lung epithelial cells
genotype: WT
treatment: KRAS-induced
Treatment protocol SAEC cells treated with 0.1 μM of 4OHT (Abcam) for 3 days to induce KRASG12V. 100 μM of DRB was added for 1.5h before harvesting.
Growth protocol SAECs (human small airway epithelial cells) were immortalized via expression of hTERT, CDK4 mutants, and cyclin D1, and retrovirally established 4-hydroxytamoxifen (4OHT)-induced KRASG12V. SAECs cell lines were cultured in BronchiaLife™ Epithelial Basal Medium (Lifeline Cell Technology) supplemented with the components of a LifeFactors® Kit (Lifeline Cell Technology). All cells were cultured at 37°C in 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated by an RNeasy mini kit (Qiagen, Germany) from each cell lysate according to the manufacturer's protocol
Strand-specific method to incorporate dUTP during synthesis of 2nd cDNA strand
DNBSEQ 2x150 bp
 
Library strategy ssRNA-seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-G400
 
Data processing Single-end sequenced reads were checked by FastQC.
Mapping was performed using Kallisto (ver. 0.46.0).
The expression matrix was constructed and normlized by tximport package (ver. 1.18.0)
Assembly: hg19
Supplementary files format and content: GEO_processed _data_BS.txt
 
Submission date Jan 17, 2023
Last update date Jun 30, 2023
Contact name Bunsyo Shiotani
E-mail(s) bshiotan@ncc.go.jp
Organization name National Cancer Center
Department Research Institute
Lab Lab of Genome Stress Signaling
Street address 5-1-1 Tuskiji
City Chuo-ku
State/province Tokyo
ZIP/Postal code 104-0045
Country Japan
 
Platform ID GPL28038
Series (1)
GSE223027 Effect of transcription inhibitor DRB on gene expression under KRASG12V induction of SAEC
Relations
BioSample SAMN32767947
SRA SRX19050197

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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