|
| Status |
Public on Oct 24, 2023 |
| Title |
WT_3D_4 |
| Sample type |
SRA |
| |
|
| Source name |
Lens epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lens epithelial cells
cell line: 21EM15
protocol: 3D
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from 2D and 3D sample have been extracted with the Nucleospin kit (Macherey-Nagel) and the RNA from the microdissection (internal and external part) were extracted with a specific kit, the Arcturus PicoPure (ThermoFisher)
3’ end seq library were prepared using the QuantSeq 3’ mRNA-Seq library Kit (Lexogen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
3D
DEA_tab_WT_2D_vs_3D.csv
|
| Data processing |
Only sens reads are use for this analysis since the library correspond to 3’end RNA-seq
reads were trimmed following lexogene suggestion, the adaptator and the polyA tail, only read with a length superior to 20 nt were kept
Trimmed reads were map to the mouse genome (GRCm38.p6) with STAR software (2.7.8a)
Uniquely mapped reads were count by featureCount (v1.6.0)
Supplementary files format and content: GRCm38.p6
Supplementary files format and content: Differential expression analysis by edgr, with cpm (count per millions) normaliezd for each sample and statistical Gene Expression difference for each genes.
|
| |
|
| Submission date |
Mar 30, 2023 |
| Last update date |
Oct 24, 2023 |
| Contact name |
Luc Paillard |
| E-mail(s) |
luc.paillard@univ-rennes.fr
|
| Organization name |
Univ Rennes
|
| Department |
IGDR (UMR6290)
|
| Lab |
EGD team
|
| Street address |
2 Ave Leon Bernard
|
| City |
Rennes |
| State/province |
Brittany |
| ZIP/Postal code |
35000 |
| Country |
France |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE228547 |
Eye lens organoids going simple: characterization of a new model |
|
| Relations |
| BioSample |
SAMN33984460 |
| SRA |
SRX19818517 |
