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Sample GSM7766062 Query DataSets for GSM7766062
Status Public on May 24, 2024
Title G_Phe
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: Phe-GAA-5'
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 SAMN37316316
SRA SRX21659604

Supplementary file Size Download File type/resource
GSM7766062_G_Phe_L1_R1_001_jC5FI0Nz37J5_expression_values.xlsx 11.8 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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