NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5345084 Query DataSets for GSM5345084
Status Public on Sep 27, 2021
Title A431-NR2F2-KD2-NO-DOX-2
Sample type SRA
 
Source name Skin squamous cell carcinoma
Organism Homo sapiens
Characteristics cell line: A431
cell type: Skin squamous cell carcinoma
treatment: None
Treatment protocol NR2F2 KD induced cells were exposed to 1µg/mL Doxycycline for 72h.
Growth protocol Cells were grown in EMEM culture medium, with 10% FBS tetracycline-free.
Extracted molecule total RNA
Extraction protocol RNA extraction from cells was performed using RNeasy micro kit (QIAGEN) according to the manufacturer ́s recommendations.
Indexed cDNA libraries were obtained using the Truseq Standard mRNA library prep kit (Illumina) .
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
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 human reference genome (Grch38.87) 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: Grch38.87
Supplementary_files_format_and_content: .txt / rawcount of gene expression
 
Submission date May 28, 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)
GSE164605 NR2F2 controls malignant squamous cell carcinoma state by promoting stemness and invasion and repressing differentiation
GSE175726 NR2F2 controls malignant squamous cell carcinoma state by promoting stemness and invasion and repressing differentiation V
Relations
BioSample SAMN19401993
SRA SRX11014513

Supplementary file Size Download File type/resource
GSM5345084_A431-NR2F2-KD2-NO-DOX-2.count.txt.gz 203.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.