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Status |
Public on Sep 27, 2021 |
Title |
A431-NR2F2-KD1-NO-DOX-1 |
Sample type |
SRA |
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|
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) .
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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
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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 |
SAMN19401996 |
SRA |
SRX11014510 |