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Sample GSM5014498 Query DataSets for GSM5014498
Status Public on Sep 27, 2021
Title WT control 2
Sample type SRA
 
Source name human lung SCC cell line (Sk-MES-1)
Organism Homo sapiens
Characteristics genotype: NR2F2 WT
Extracted molecule total RNA
Extraction protocol RNA extraction from cultured cells was performed using RNeasy micro kit (QIAGEN) according to the manufacturer ́s recommendations.
Indexed cDNA libraries were obtained using the Ovation Solo RNA-seq Systems (NuGen) following manufacturer’s recommendations.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description MMI14
Data processing Adaptors sequences were removed with TrimmomaticPE using options “ILLUMINACLIP:adaptor.file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:8”
Reads were mapped against the mouse reference genome (hg38/GRCh87) using STAR software
Duplicate reads were removed by Picard tools, MarkDuplicates module.
After transcripts assembling, gene level counts were obtained using Htseq with annotations GRCh38.87 and normalized to 20 millions of aligned reads.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: .csv / Normalized gene expression
 
Submission date Jan 11, 2021
Last update date Sep 27, 2021
Contact name Yura Song
E-mail(s) yura.song@ulb.be
Organization name Université Libre de Bruxelles
Lab Laboratory of Stem Cells and Cancer
Street address 808, route de Lennik
City Bruxelles
ZIP/Postal code 1070
Country Belgium
 
Platform ID GPL24676
Series (2)
GSE164592 NR2F2 is an essential regulator of malignant tumor state by promoting tumor stemness, invasion and repressing differentiation I
GSE164605 NR2F2 controls malignant squamous cell carcinoma state by promoting stemness and invasion and repressing differentiation
Relations
BioSample SAMN17284412
SRA SRX9822636

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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