|
| Status |
Public on May 24, 2024 |
| Title |
E_CT |
| Sample type |
SRA |
| |
|
| Source name |
Islets of Langerhans
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Islets of Langerhans
age: 12-weeks
cell type: Beta-cells and alpha-cells mainly
genotype: C57BL/6NRj mice
treatment: Control
|
| Treatment protocol |
Dissociated mouse islet cells were transfected using Lipofectamine 2000 (Thermo Fisher) with scramble control oligonucleotides or specific tRF mimics for LysCTT-5’, PheGAA-5’ and SerGCT-3’ (Integrated DNA Technologies). RNA was collected in Qiazol (Qiagen), 48h after transfection
|
| Growth protocol |
Mouse pancreases from C57BL/6NRj mice were digested with collagenase (Sigma), and islets isolated by Histopaque (Sigma) density gradient and handpicking. Purified islet cells were cultured in RPMI 1640 GlutaMAX medium (ThermoFisher) supplemented with 10% FCS, 100 U/mL penicillin and 100 µg/mL streptomycin, 1 mM sodium pyruvate (Sigma), and 10 mM Hepes (Sigma). Rodent islets were dissociated into single cells by incubation in Ca2+/Mg2+free phosphate-buffered saline, 3 mM EGTA, and 0.002% trypsin (ThermoFisher) for 2-3 min at 37 °C and cultured 24h before treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with miRNeasy kit (Qiagen).
Illumina stranded mRNA prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Expression values
|
| Data processing |
The analysis was performed using the QIAGEN RNA-seq Analysis Portal 4.1
Assembly: GRCm38
Supplementary files format and content: tab-delimited xlsx files include RNA TPM, RPKM and CPM values
|
| |
|
| Submission date |
Sep 07, 2023 |
| Last update date |
May 24, 2024 |
| Contact name |
Flora Brozzi |
| E-mail(s) |
florabrozzi@gmail.com
|
| Organization name |
University of Lausanne
|
| Department |
DNF
|
| Lab |
Regazzi's
|
| Street address |
Rue du Bugnon 9
|
| City |
Lausanne |
| ZIP/Postal code |
1005 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE242561 |
Role of tRNA-derived fragments in the cross-talk between immune cells and beta cells during type 1 diabetes pathogenesis (tRF overexpression) |
| GSE242568 |
Role of tRNA-derived fragments in the cross-talk between immune cells and beta cells during type 1 diabetes pathogenesis |
|
| Relations |
| BioSample |
SAMN37316318 |
| SRA |
SRX21659602 |
