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Sample GSM7461362 Query DataSets for GSM7461362
Status Public on Jun 13, 2023
Title EP+ KD Unc5b 1
Sample type SRA
 
Source name skin
Organism Mus musculus
Characteristics tissue: skin
cell line: LKPR EPCAM+
cell type: Epithelial cells
genotype: Lgr5CreER/ KrasLSL-G12D/p53fl/fl/Rosa26-YFP+/+
treatment: Unc5b Knock-down
Extracted molecule total RNA
Extraction protocol RNA extraction from FACS-isolated cells was performed using RNeasy micro kit (QIAGEN) according to the manufacturer’s recommendations.
Indexed complementary DNA 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 JLE3-KDUNC5B-1-Day6-10
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 (Grcm38/mm10) using STAR software
Duplicate reads were removed by Picard tools, MarkDuplicates module.
After transcripts assembling, gene level counts were obtained using Htseq with annotations Grcm38.87 and normalized to 20 millions of aligned reads.
Assembly: Mm10 / Grcm38.87
Supplementary files format and content: .csv / normalized gene expression with annotation
 
Submission date Jun 06, 2023
Last update date Jun 13, 2023
Contact name Sebastiaan Vanuytven
E-mail(s) sebastiaan.vanuytven@ulb.be
Organization name Université Libre de Bruxelles
Street address Campus Erasme CP 637
City Brussels
ZIP/Postal code 1000
Country Belgium
 
Platform ID GPL24247
Series (2)
GSE234263 Pharmacological targeting Netrin-1 inhibits EMT in cancer [BulkRNA-seq]
GSE234267 Pharmacological targeting Netrin-1 inhibits EMT in cancer
Relations
BioSample SAMN35646892
SRA SRX20611783

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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