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Status |
Public on Apr 22, 2024 |
Title |
Human esophageal squamous cell carcinoma cells (KYSE70) without treatment, replicate 1 |
Sample type |
SRA |
|
|
Source name |
Human esophageal squamous cell carcinoma cells (KYSE70)
|
Organism |
Homo sapiens |
Characteristics |
cell line: KYSE70 cell type: esophageal squamous cell carcinoma cells treatment: untreated
|
Treatment protocol |
The cells were treated with 10 µM pyrimethamine or 20 nM mitoxantrone for 72 h.
|
Growth protocol |
The cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum, 50 U/ml penicillin, and 50 µg/ml streptomycin at 37°C in 5% CO2/95% air.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from human esophageal squamous cell carcinoma cells (KYSE70) using RNeasy Kit (Qiagen; Valencia, CA). RNA libraries were prepared for sequencing using standard Illumina protocols
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|
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
K70_1
|
Data processing |
The data quality was assessed with FastQC (version 0.11.5), low-quality reads were removed, and remaining adapter sequences were hard clipped with cutadapt (version 1.12) whenever applicable. The quality filtered reads were aligned with STAR (version 2.6.90c) to human reference genome (hg38) with its respective RefSeq annotation, at last, the expression levels of genes were obtained with FeatureCounts (version 1.5.1). Genome_build: hg38 Supplementary_files_format_and_content: tab-delimited text files for each Sample
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Submission date |
Apr 23, 2021 |
Last update date |
Apr 22, 2024 |
Contact name |
Xiaoxin Luke Chen |
E-mail(s) |
lchen@Coriell.org
|
Organization name |
Coriell Institute for Medical Research
|
Lab |
Chen
|
Street address |
403 Haddon Ave
|
City |
Camden |
State/province |
NJ |
ZIP/Postal code |
08103 |
Country |
USA |
|
|
Platform ID |
GPL24676 |
Series (1) |
GSE173164 |
To investigate the effects of NRF2 inhibitors (pyrimethamine and mitoxantrone) on gene expression in a human esophageal squamous cell carcinoma cell line (KYSE70) |
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Relations |
BioSample |
SAMN18839249 |
SRA |
SRX10664002 |