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Sample GSM6318416 Query DataSets for GSM6318416
Status Public on May 29, 2024
Title Pancreas, hand-picked pancreatic islets, 2-weeks high-fat diet, Ide+/+ C57BL/6J, biol rep5
Sample type SRA
 
Source name Pancreas
Organism Mus musculus
Characteristics tissue: Pancreas
strain: C57BL/6J
cell type: Hand-picked pancreatic islets
Sex: Female
genotype: Ide+/+
treatment: 2-weeks high-fat diet
age at_treatment_initiation: 10 weeks-old
Treatment protocol 10-weeks-old female Ide-/- and Ide+/+ C57BL/6J mice were fed with a high-fat diet for 2 weeks (D12492. Rodent Diet With 60 kcal% Fat, Brogaarden, Denmark).
Extracted molecule total RNA
Extraction protocol RNA was harvested using Rneasy mini plus kit (Qiagen). 100 ng of high-quality total RNA sample (RIN>6.5) was used for the construction of sequencing libraries.
RNA-seq libraries for RNA-seq were prepared using NEBNext low input RNA library prep kit (NEB) according to manufacturer's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Sequence reads were mapped to GRCm38 from Ensembl release 101 using STAR v.2.7.1a with the following parameters : --twopassMode Basic --sjdbOverhang 74 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMunmapped Within --outFilterType BySJout --quantMode TranscriptomeSAM
Read count were performed using RSEM v1.3.1) with the AlignedtoTranscriptome bam files from STAR
Supplementary files format and content: tab-delimited text files including RSEM expected count, FPKM and TPM values for each sample
 
Submission date Jul 08, 2022
Last update date May 29, 2024
Contact name François-Xavier MAUVAIS
E-mail(s) francois-xavier.mauvais@inserm.fr
Organization name INSERM
Department U1151
Lab van Endert
Street address 160 rue de Vaugirard
City Paris
ZIP/Postal code 75015
Country France
 
Platform ID GPL19057
Series (1)
GSE207797 Effect of depletion of IDE on gene expression in adult pancreatic islets during a metabolic stress
Relations
BioSample SAMN29613458
SRA SRX16101788

Supplementary file Size Download File type/resource
GSM6318416_WT2-5_S5.resultsRSEM.genes.results.gz 1.1 Mb (ftp)(http) RESULTS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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