|
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.
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|
|
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
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|
|
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 |