|
| Status |
Public on Jun 13, 2023 |
| Title |
EP+ KD Ntn1 2 |
| 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: Netrin-1 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 |
JLE6-KDNTN1-2-Day6-14
|
| 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 |
SAMN35646889 |
| SRA |
SRX20611786 |
